SJ1 Metatranscriptomes
Andrew St. James, Elisha WC, Zach Crockett
Generated July 8, 2020

Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions

Andrew R. St. James* and Ruth E. Richardson

*Author/Owner of KBase Narratives

This Narrative is part of a collection used in a single publication. The paper took a metagnomic and metatranscriptomic approach to examine a bioreactor's response to the presence of sulfate, which reduces the production of methane, a valuable product, while producing hydrogen sulfide, a corrosive contaminant.

This Narrative collection has been created to highlight the types of analyses done for this publication. They are as follows (in order):

Please cite: Andrew R St. James, Ruth E Richardson. Ecogenomics reveals community interactions in a long-term methanogenic bioreactor and a rapid switch to sulfate-reducing conditions, FEMS Microbiology Ecology, Volume 96, Issue 5, May 2020, https://doi.org/10.1093/femsec/fiaa050.

Workflow Narrative 2: Metatranscriptomics Analysis

Background

Discussion of paper

In this Narrative, metatranscriptomic reads were aligned to individual MAGs isolated from the previous Narrative.

For a more complete summary of the publication, please see this Narrative.

Metadata about the sequencing libraries is found in the following table:

Sequencing Library GOLD analysis project ID # Reads (post-QC) # Contigs N50
SJ1 Metagenome Ga0228535 222,599,058 212,269 2,212
SJ1S Metagenome Ga0228536 196,244,686 171,234 2,141
‘Starvation’ Metatranscriptome Ga0232079 30,039,006 — —
‘Control’ Metatranscriptome (6 h) Ga0232080 62,907,116 — —
‘Control’ Metatranscriptome (24 h) Ga0247507 66,383,206 — —
‘Control’ Metatranscriptome (48 h) Ga0232081 49,369,646 — —
‘Sulfate Provision’ Metatranscriptome (6 h) Ga0232082 69,051,286 — —
‘Sulfate Provision’ Metatranscriptome (24 h) Ga0247508 61,969,624 — —
‘Sulfate Provision’ Metatranscriptome (48 h) Ga0247509 50,036,086 — —

Preparation

Sequencing was performed at JGI using standard pipelines. QC-filtered reads were generated and upload to KBase here.

Narrative Table of Contents

Metatranscriptomics TOC

  1. Importing Reads
  2. Create RNA-seq Sample Set
  3. Aligning Reads to Reference Genome Using Bowtie2
  4. Assembling Transcripts Using Cufflinks
  5. Creating Differential Expression with Cuffdiff and Miscellaneous Exploratory Analyses
  6. Supplementary Information

Importing Reads from Staging

Reads were imported from files described in the paper using the App cells below.

Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 16s.
Objects
Created Object Name Type Description
SJ1_C12.fastq_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 19s.
Objects
Created Object Name Type Description
SJ1_S12.fastq_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 5m 9s.
Objects
Created Object Name Type Description
SJ1_C0.fastq_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 16m 16s.
Objects
Created Object Name Type Description
SJ1_S4.fastq_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 16m 16s.
Objects
Created Object Name Type Description
SJ1_C4.filter-MTF.fastq_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 20s.
Objects
Created Object Name Type Description
SJ1_C36.fastq_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly
Import FASTQ/SRA File as Reads from Staging Area
Import a FASTQ/SRA file into your Narrative as a Reads data object
This app completed without errors in 11m 17s.
Objects
Created Object Name Type Description
SJ1_S36.fastq_reads PairedEndLibrary Imported Reads
Report
Links
  • report.html - HTML summary report for Imported Assembly

Creating RNA-seq Sample Sets

Previously imported reads were grouped into sets of reads using the Create RNA-seq Sample Set App.

Create RNA-seq Sample Set
Provide RNA-seq reads and the metadata to create an RNA-seq Sample Set
This app completed without errors in 1m 4s.
No output found.
Output from Create RNA-seq Sample Set
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Create RNA-seq Sample Set
Provide RNA-seq reads and the metadata to create an RNA-seq Sample Set
This app completed without errors in 10s.
No output found.
Output from Create RNA-seq Sample Set
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Create RNA-seq Sample Set
Provide RNA-seq reads and the metadata to create an RNA-seq Sample Set
This app completed without errors in 4s.
No output found.
Output from Create RNA-seq Sample Set
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937

Align Reads to Reference Genome Using Bowtie2

The reads were then aligned to the reference genomes created in the SJ1 metagenome Narrative build genomeset using Bowtie2.

Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 4h 58m 23s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 3h 50m 17s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 5h 43m 55s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 3h 53m 47s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 4h 8m 42s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 4h 3m 8s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 3h 57m 49s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 3h 43m 55s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 4h 22m 46s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 3h 57m 49s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 3h 58m 50s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 4h 23m 1s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 4h 18m 7s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 4h 43m 52s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app produced errors in 2h 2m 35s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app produced errors in 3h 26m 31s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app produced errors in 2h 24m 14s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app produced errors in 2h 28m 59s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app produced errors in 2h 11m 30s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app produced errors in 2h 26m 32s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app produced errors in 2h 39m 10s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app produced errors in 2h 17m 34s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 1h 57m 9s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 1h 59m 35s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 2h 15m 41s.
No output found.
Align Reads using Bowtie2 v2.3.2
Align sequencing reads to long reference prokaryotic genome sequences using Bowtie2
This app completed without errors in 2h 5m 40s.
No output found.

Assemble transcripts using Cufflinks

The transcript alignment sets were then assembled using Cufflinks. One exploratory run was submitted with StringTie, but resulted in an error and StringTie assembly was not pursued any further.

Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 1h 0m 9s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_15_expression_set_15 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_15_expression_15 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_15_expression_15 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_15_expression_15 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_15_expression_15 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_15_expression_15 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_15_expression_15 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_15_expression_15 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_15_15_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_15_15_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 1h 18m 22s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_02_expression_set_02 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_02_expression_02 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_02_expression_02 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_02_expression_02 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_02_expression_02 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_02_expression_02 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_02_expression_02 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_02_expression_02 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_02_02_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_02_02_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 1h 2m 40s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_05_expression_set_05 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_05_expression_05 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_05_expression_05 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_05_expression_05 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_05_expression_05 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_05_expression_05 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_05_expression_05 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_05_expression_05 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_05_05_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_05_05_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 50m 3s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_03_expression_set_03 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_03_expression_03 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_03_expression_03 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_03_expression_03 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_03_expression_03 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_03_expression_03 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_03_expression_03 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_03_expression_03 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_03_03_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_03_03_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 1h 0m 18s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_01_expression_set_01 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_01_01_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_01_01_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 48m 56s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_08_expression_set_08 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_08_expression_08 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_08_expression_08 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_08_expression_08 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_08_expression_08 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_08_expression_08 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_08_expression_08 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_08_expression_08 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_08_08_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_08_08_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 49m 25s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_60_expression_set_60 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_60_expression_60 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_60_expression_60 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_60_expression_60 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_60_expression_60 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_60_expression_60 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_60_expression_60 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_60_expression_60 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_60_60_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_60_60_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 2h 35m 2s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_61_expression_set_61 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_61_expression_61 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_61_expression_61 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_61_expression_61 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_61_expression_61 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_61_expression_61 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_61_expression_61 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_61_expression_61 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_61_61_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_61_61_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 59m 50s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_25_expression_set_25 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_25_expression_25 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_25_expression_25 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_25_expression_25 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_25_expression_25 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_25_expression_25 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_25_expression_25 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_25_expression_25 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_25_25_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_25_25_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 53m 59s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_22_expression_set_22 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_22_expression_22 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_22_expression_22 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_22_expression_22 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_22_expression_22 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_22_expression_22 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_22_expression_22 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_22_expression_22 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_22_22_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_22_22_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 49m 33s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_06_expression_set_06 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_06_expression_06 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_06_expression_06 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_06_expression_06 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_06_expression_06 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_06_expression_06 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_06_expression_06 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_06_expression_06 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_06_06_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_06_06_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 1h 1m 24s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_10_expression_set_10 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_10_expression_10 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_10_expression_10 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_10_expression_10 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_10_expression_10 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_10_expression_10 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_10_expression_10 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_10_expression_10 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_10_10_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_10_10_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 1h 0m 18s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_04_expression_set_04 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_04_expression_04 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_04_expression_04 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_04_expression_04 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_04_expression_04 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_04_expression_04 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_04_expression_04 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_04_expression_04 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_04_04_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_04_04_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 46m 57s.
Objects
Created Object Name Type Description
SJ1_BaselineControlSulfate_alignment_set_01_expression_set_01 ExpressionSet ExpressionSet generated by Cufflinks
SJ1_C4.filter-MTF.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_C12.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_C36.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_C0.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_S4.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_S12.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_S36.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_01_01_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
SJ1_BaselineControlSulfate_alignment_set_01_01_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 23m 10s.
Objects
Created Object Name Type Description
MT_4vS4_alignment_set_02_expression_set_02 ExpressionSet ExpressionSet generated by Cufflinks
12293.3.250296.CGATGT.filter-MTF.fastq_reads_alignment_02_expression_02 RNASeqExpression Expression generated by Cufflinks
12293.4.250301.ACAGTG.filter-MTF.fastq_reads_alignment_02_expression_02 RNASeqExpression Expression generated by Cufflinks
MT_4vS4_alignment_set_02_02_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
MT_4vS4_alignment_set_02_02_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 14m 18s.
Objects
Created Object Name Type Description
MT_4vS4_alignment_set_05_expression_set_05 ExpressionSet ExpressionSet generated by Cufflinks
12293.3.250296.CGATGT.filter-MTF.fastq_reads_alignment_05_expression_05 RNASeqExpression Expression generated by Cufflinks
12293.4.250301.ACAGTG.filter-MTF.fastq_reads_alignment_05_expression_05 RNASeqExpression Expression generated by Cufflinks
MT_4vS4_alignment_set_05_05_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
MT_4vS4_alignment_set_05_05_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 15m 56s.
Objects
Created Object Name Type Description
MT_4vS4_alignment_set_04_expression_set_04 ExpressionSet ExpressionSet generated by Cufflinks
12293.3.250296.CGATGT.filter-MTF.fastq_reads_alignment_04_expression_04 RNASeqExpression Expression generated by Cufflinks
12293.4.250301.ACAGTG.filter-MTF.fastq_reads_alignment_04_expression_04 RNASeqExpression Expression generated by Cufflinks
MT_4vS4_alignment_set_04_04_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
MT_4vS4_alignment_set_04_04_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 14m 59s.
Objects
Created Object Name Type Description
MT_4vS4_alignment_set_10_expression_set_10 ExpressionSet ExpressionSet generated by Cufflinks
12293.3.250296.CGATGT.filter-MTF.fastq_reads_alignment_10_expression_10 RNASeqExpression Expression generated by Cufflinks
12293.4.250301.ACAGTG.filter-MTF.fastq_reads_alignment_10_expression_10 RNASeqExpression Expression generated by Cufflinks
MT_4vS4_alignment_set_10_10_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
MT_4vS4_alignment_set_10_10_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 20m 41s.
Objects
Created Object Name Type Description
MT_4vS4_alignment_set_01_expression_set_01 ExpressionSet ExpressionSet generated by Cufflinks
12293.3.250296.CGATGT.filter-MTF.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
12293.4.250301.ACAGTG.filter-MTF.fastq_reads_alignment_01_expression_01 RNASeqExpression Expression generated by Cufflinks
MT_4vS4_alignment_set_01_01_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
MT_4vS4_alignment_set_01_01_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app completed without errors in 15m 29s.
Objects
Created Object Name Type Description
MT_4vS4_alignment_set_08_expression_set ExpressionSet ExpressionSet generated by Cufflinks
12293.3.250296.CGATGT.filter-MTF.fastq_reads_alignment_08_expression RNASeqExpression Expression generated by Cufflinks
12293.4.250301.ACAGTG.filter-MTF.fastq_reads_alignment_08_expression RNASeqExpression Expression generated by Cufflinks
MT_4vS4_alignment_set_08_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by Cufflinks
MT_4vS4_alignment_set_08_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by Cufflinks
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/30937
  • cufflinks_result.zip - File(s) generated by Cufflinks App
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app produced errors in 7m 12s.
No output found.
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app produced errors in 6m 19s.
No output found.
Output from Assemble Transcripts using Cufflinks - v2.2.1
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app produced errors in 7m 1s.
No output found.
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app produced errors in 9m 13s.
No output found.
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app produced errors in 1d 5h 59m 14s.
No output found.
Assemble Transcripts using Cufflinks - v2.2.1
Assemble the transcripts from RNA-seq reads using Cufflinks.
This app produced errors in 1d 23h 54m 25s.
No output found.
Assemble Transcripts using StringTie - v1.0.8
Assemble the transcripts from RNA-seq reads using StringTie
This app produced errors in 3m 23s.
No output found.

Creating Differential Expression Using Cuffdiff and Miscellaneous Exploratory Analyses

StringTie-assembled transcripts were used in Cuffdiff to generate differential expression matrices, but the analyses were unsuccessful. The remainder of this Narrative was for exploratory analyses.

Create Differential Expression using Cuffdiff - v2.2.1
Identify significant changes in the gene and transcript expression level using Cuffdiff
This app produced errors in 14m 33s.
No output found.
Create Differential Expression using Cuffdiff - v2.2.1
Identify significant changes in the gene and transcript expression level using Cuffdiff
This app produced errors in 20m 59s.
No output found.
Create Differential Expression using Cuffdiff - v2.2.1
Identify significant changes in the gene and transcript expression level using Cuffdiff
This app produced errors in 20m 53s.
No output found.
Create Differential Expression using Cuffdiff - v2.2.1
Identify significant changes in the gene and transcript expression level using Cuffdiff
This app produced errors in 19m 53s.
No output found.
Create Differential Expression using Cuffdiff - v2.2.1
Identify significant changes in the gene and transcript expression level using Cuffdiff
This app produced errors in 5m 39s.
No output found.
Create Differential Expression using Cuffdiff - v2.2.1
Identify significant changes in the gene and transcript expression level using Cuffdiff
This app produced errors in 7m 26s.
No output found.
Create Differential Expression Matrix using Ballgown
Create differential expression matrix based on a given threshold cutoff
This app produced errors in 31s.
No output found.
Create Differential Expression Matrix using DESeq2 - v1.0.3
Create differential expression matrix based on a given threshold cutoff
This app produced errors in 1m 15s.
No output found.
from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_local_app(
    "KBaseFeatureValues/view_expression_gene_table_heatmap",
    {
    "input_expression_matrix": "MT_4vS4_alignment_set_03_FPKM_ExpressionMatrix",
    "input_condition_ids": []
},
    tag="release",
    version="0.0.17",
    cell_id="fa67a90f-a94b-4b5d-a204-919485988f81",
    run_id="f12c9a2f-1cb6-4cb2-ae24-c0667544f77f"
)
Out[7]:
View P-value Distribution for Differential Expression
Display the P-value distribution of differentially expressed genes to filter an expression matrix based on P-value cutoff or number of features.
This app completed without errors in 12s.
No output found.
Output from View P-value Distribution for Differential Expression
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
C4vS4_03_FPKM_pValue.fdt
v1 - MAK.FloatDataTable-2.1
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
C4vS4_03_FPKM_pValue
v1 - CoExpression.FigureProperties-1.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
Insert Genome Into Species Tree
Add one or more genomes to a KBase species tree.
This app produced errors in 2m 54s.
No output found.
Output from Insert Genome Into Species Tree
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
12293.3.250296.CGATGT.filter-MTF.fastq_reads_alignment_C4_Bin03
v1 - KBaseRNASeq.RNASeqAlignment-3.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
MT_4vS4
v1 - KBaseRNASeq.RNASeqSampleSet-1.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
12293.3.250296.CGATGT.filter-MTF.fastq_reads_alignment
v3 - KBaseRNASeq.RNASeqAlignment-3.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
12293.4.250301.ACAGTG.filter-MTF.fastq_reads_alignment
v2 - KBaseRNASeq.RNASeqAlignment-3.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
MT_4vS4
v1 - KBaseRNASeq.RNASeqSampleSet-1.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
06_Desulfovibrio_GTF_Annotation
v2 - KBaseRNASeq.GFFAnnotation-2.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
MT_4vS4_alignment_set
v2 - KBaseSets.ReadsAlignmentSet-1.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
12293.3.250296.CGATGT.filter-MTF.fastq_reads_alignment_C4_Bin03
v1 - KBaseRNASeq.RNASeqAlignment-3.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937
MT_4vS4_alignment_set
v2 - KBaseSets.ReadsAlignmentSet-1.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/30937

Supplementary Information

The objects contained in this Narrative as well as the key objects used for all analyses in the publication can be viewed and copied for further analysis in the SJ1 Intermediate Files Narrative.

Apps

  1. Align Reads using Bowtie2 - v2.3.2
    • Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9: 357 359. doi:10.1038/nmeth.1923
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10: R25. doi:10.1186/gb-2009-10-3-r25
  2. Assemble Transcripts using Cufflinks - v2.2.1
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 2013;14: R36. doi:10.1186/gb-2013-14-4-r36
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10: R25. doi:10.1186/gb-2009-10-3-r25
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25: 1105 1111. doi:10.1093/bioinformatics/btp120
    • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7: 562 578. doi:10.1038/nprot.2012.016
  3. Assemble Transcripts using StringTie - v1.3.3b
    • Pertea M, Pertea GM, Antonescu CM, Chang TC, Mendell JT & Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads Nature Biotechnology 2015
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL (2013) TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 14:R36
    • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter, L (2012) Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols, 7(3), 562 578.
    • Trapnell C, Pachter L, Salzberg SL. (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. Vol 25, 9:1105-1111.
    • Frazee, A. C., Pertea, G., Jaffe, A. E., Langmead, B., Salzberg, S. L., & Leek, J. T. (2015). Ballgown bridges the gap between transcriptome assembly and expression analysis. Nature Biotechnology, 33(3), 243 246.
  4. Create Differential Expression Matrix using Ballgown - v3.5
    no citations
  5. Create Differential Expression Matrix using DESeq2 - v1.20.0
    • Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology. 2014;15: 550. doi:10.1186/s13059-014-0550-8
  6. Create Differential Expression using Cuffdiff - v2.2.1
    • Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg SL. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biology. 2013;14: R36. doi:10.1186/gb-2013-14-4-r36
    • Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10: R25. doi:10.1186/gb-2009-10-3-r25
    • Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25: 1105 1111. doi:10.1093/bioinformatics/btp120
    • Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, et al. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc. 2012;7: 562 578. doi:10.1038/nprot.2012.016
  7. Create RNA-seq Sample Set
    no citations
  8. Import FASTQ/SRA File as Reads from Staging Area
    no citations
  9. Insert Genome Into SpeciesTree - v2.2.0
    • Price MN, Dehal PS, Arkin AP. FastTree 2 Approximately Maximum-Likelihood Trees for Large Alignments. PLoS One. 2010;5. doi:10.1371/journal.pone.0009490
  10. View P-value Distribution for Differential Expression
    no citations