tRNA_Modification_mutants_RNAseq_E.coli
Jill Babor, Jo Marie Bacusmo, Valerie de Crecy-Lagard, yifeng yuan
Generated November 7, 2024

RNA-seq analysis of nine tRNA-modification deficient mutants in Escherichia coli K12 substr. BW25113

Triplicate paired-end reads for each strain were grouped, trimmed (head crop length = 9; low quality reads removed), assessed for quality by FastQC, and aligned to an annotated E. coli K12 substr. BW25113 genome using HISAT2. Transcripts were assembled using StringTie and differential expression between strains was assessed using DeSeq2.

All reads, the annotated reference genome and all data generated can be found in the narrative data tab.

Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 2h 43m 4s.
Objects
Created Object Name Type Description
WT_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
WT_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
WT_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
WT_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
WT_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
WT_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 7h 20m 36s.
Objects
Created Object Name Type Description
trmJ_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
trmJ_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
trmJ_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
trmJ_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
trmJ_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
trmJ_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 6h 50m 21s.
Objects
Created Object Name Type Description
dusB_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
dusB_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
dusB_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
dusB_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
dusB_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
dusB_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 6h 35m 8s.
Objects
Created Object Name Type Description
truD_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
truD_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
truD_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
truD_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
truD_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
truD_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 3h 4m 22s.
Objects
Created Object Name Type Description
miaA_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
miaA_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
miaA_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
miaA_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
miaA_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
miaA_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 6h 34m 16s.
Objects
Created Object Name Type Description
rlmN_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
rlmN_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
rlmN_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
rlmN_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
rlmN_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
rlmN_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 5h 29m 27s.
Objects
Created Object Name Type Description
thiI_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
thiI_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
thiI_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
thiI_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
thiI_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
thiI_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 4h 11m 50s.
Objects
Created Object Name Type Description
mnmA_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
mnmA_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
mnmA_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
mnmA_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
mnmA_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
mnmA_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 2h 6m 2s.
Objects
Created Object Name Type Description
mnmG_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
mnmG_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
mnmG_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
mnmG_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
mnmG_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
mnmG_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 6h 47m 50s.
Objects
Created Object Name Type Description
mnmC_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
mnmC_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
mnmC_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
mnmC_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
mnmC_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
mnmC_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 5h 1m 30s.
Objects
Created Object Name Type Description
truA_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
truA_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
truA_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
truA_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
truA_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
truA_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Trim Reads with Trimmomatic - v0.36
Trim paired- or single-end Illumina reads with Trimmomatic.
This app completed without errors in 6h 25m 36s.
Objects
Created Object Name Type Description
thiI_SampleSet_Trimmed_trimm_paired ReadsSet Trimmed Reads
thiI_SampleSet_Trimmed_trimm_paired_SampleSet RNASeqSampleSet Trimmed Reads
thiI_SampleSet_Trimmed_trimm_unpaired_fwd ReadsSet Trimmed Unpaired Forward Reads
thiI_SampleSet_Trimmed_trimm_unpaired_fwd_SampleSet RNASeqSampleSet Trimmed Unpaired Forward Reads
thiI_SampleSet_Trimmed_trimm_unpaired_rev ReadsSet Trimmed Unpaired Reverse Reads
thiI_SampleSet_Trimmed_trimm_unpaired_rev_SampleSet RNASeqSampleSet Trimmed Unpaired Reverse Reads
Report
Links
Create RNA-seq SampleSet
Allows users to provide RNA-seq reads and the corresponding metadata to create an RNASeqSampleSet data object.
This app completed without errors in 7s.
No output found.
Output from Create RNA-seq SampleSet
The viewer for the output created by this App is available at the original Narrative here: https://narrative.kbase.us/narrative/197146
Assess Read Quality with FastQC - v0.11.9
A quality control application for high throughput sequence data.
This app completed without errors in 1d 0h 53m 36s.
Report
Links
  • index.html - HTML files generated by fastqc that contains report on quality of reads
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/197146
  • trmJ_R2_reads_trimm_paired_101487_116_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • miaA_R1_reads_trimm_paired_101487_129_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truD_R2_reads_trimm_paired_101487_157_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • rlmN_R1_reads_trimm_paired_101487_130_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • rlmN_R2_reads_trimm_paired_101487_154_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • rlmN_R1_reads_trimm_paired_101487_130_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • WT_R3_reads_trimm_paired_101487_106_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • thiI_R3_reads_trimm_paired_101487_237_3.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truA_R2_reads_trimm_paired_101487_239_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truA_R1_reads_trimm_paired_101487_209_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • dusB_R2_reads_trimm_paired_101487_160_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • rlmN_R3_reads_trimm_paired_101487_163_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • dusB_R3_reads_trimm_paired_101487_183_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • miaA_R3_reads_trimm_paired_101487_144_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • thiI_R2_reads_trimm_paired_101487_199_3.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • dusB_R2_reads_trimm_paired_101487_160_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmC_R1_reads_trimm_paired_101487_214_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmA_R1_reads_trimm_paired_101487_196_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • thiI_R1_reads_trimm_paired_101487_193_3.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • dusB_R1_reads_trimm_paired_101487_135_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • WT_R2_reads_trimm_paired_101487_100_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • thiI_R1_reads_trimm_paired_101487_193_3.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • miaA_R2_reads_trimm_paired_101487_141_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmA_R2_reads_trimm_paired_101487_205_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truD_R1_reads_trimm_paired_101487_138_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmC_R3_reads_trimm_paired_101487_255_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truA_R2_reads_trimm_paired_101487_239_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truA_R3_reads_trimm_paired_101487_245_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • trmJ_R1_reads_trimm_paired_101487_103_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • trmJ_R3_reads_trimm_paired_101487_119_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truD_R1_reads_trimm_paired_101487_138_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmC_R2_reads_trimm_paired_101487_242_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truD_R3_reads_trimm_paired_101487_164_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • trmJ_R1_reads_trimm_paired_101487_103_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmC_R1_reads_trimm_paired_101487_214_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmG_R1_reads_trimm_paired_101487_202_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmG_R3_reads_trimm_paired_101487_217_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmC_R3_reads_trimm_paired_101487_255_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truA_R1_reads_trimm_paired_101487_209_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmG_R3_reads_trimm_paired_101487_217_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmA_R2_reads_trimm_paired_101487_205_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • WT_R2_reads_trimm_paired_101487_100_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmC_R2_reads_trimm_paired_101487_242_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmG_R1_reads_trimm_paired_101487_202_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • WT_R3_reads_trimm_paired_101487_106_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • trmJ_R2_reads_trimm_paired_101487_116_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmG_R2_reads_trimm_paired_101487_208_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truA_R3_reads_trimm_paired_101487_245_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • trmJ_R3_reads_trimm_paired_101487_119_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • rlmN_R2_reads_trimm_paired_101487_154_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • rlmN_R3_reads_trimm_paired_101487_163_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • miaA_R2_reads_trimm_paired_101487_141_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • thiI_R3_reads_trimm_paired_101487_237_3.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • miaA_R3_reads_trimm_paired_101487_144_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • dusB_R3_reads_trimm_paired_101487_183_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmA_R3_reads_trimm_paired_101487_227_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • WT_R1_reads_trimm_paired_101487_97_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • miaA_R1_reads_trimm_paired_101487_129_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmA_R3_reads_trimm_paired_101487_227_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truD_R3_reads_trimm_paired_101487_164_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • dusB_R1_reads_trimm_paired_101487_135_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmG_R2_reads_trimm_paired_101487_208_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • mnmA_R1_reads_trimm_paired_101487_196_1.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • thiI_R2_reads_trimm_paired_101487_199_3.fwd_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • WT_R1_reads_trimm_paired_101487_97_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
  • truD_R2_reads_trimm_paired_101487_157_1.rev_fastqc.zip - Zip file generated by fastqc that contains original images seen in the report
Align Reads using HISAT2 - v2.1.0
Align sequencing reads to long reference sequences using HISAT2.
This app completed without errors in 1d 18h 39m 8s.
Objects
Created Object Name Type Description
trmJ_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/103/1 aligned to Genome 101487/2/1
miaA_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/129/1 aligned to Genome 101487/2/1
mnmG_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/202/1 aligned to Genome 101487/2/1
truD_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/164/1 aligned to Genome 101487/2/1
WT_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/106/1 aligned to Genome 101487/2/1
WT_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/97/1 aligned to Genome 101487/2/1
rlmN_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/163/1 aligned to Genome 101487/2/1
mnmA_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/205/1 aligned to Genome 101487/2/1
truA_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/239/1 aligned to Genome 101487/2/1
mnmG_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/208/1 aligned to Genome 101487/2/1
mnmC_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/214/1 aligned to Genome 101487/2/1
truA_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/209/1 aligned to Genome 101487/2/1
mnmG_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/217/1 aligned to Genome 101487/2/1
dusB_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/135/1 aligned to Genome 101487/2/1
trmJ_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/119/1 aligned to Genome 101487/2/1
mnmC_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/242/1 aligned to Genome 101487/2/1
rlmN_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/130/1 aligned to Genome 101487/2/1
miaA_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/144/1 aligned to Genome 101487/2/1
mnmC_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/255/1 aligned to Genome 101487/2/1
WT_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/100/1 aligned to Genome 101487/2/1
miaA_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/141/1 aligned to Genome 101487/2/1
thiI_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/193/3 aligned to Genome 101487/2/1
truD_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/138/1 aligned to Genome 101487/2/1
mnmA_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/227/1 aligned to Genome 101487/2/1
rlmN_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/154/1 aligned to Genome 101487/2/1
mnmA_R1_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/196/1 aligned to Genome 101487/2/1
thiI_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/237/3 aligned to Genome 101487/2/1
dusB_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/183/1 aligned to Genome 101487/2/1
thiI_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/199/3 aligned to Genome 101487/2/1
dusB_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/160/1 aligned to Genome 101487/2/1
truA_R3_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/245/1 aligned to Genome 101487/2/1
trmJ_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/116/1 aligned to Genome 101487/2/1
truD_R2_reads_trimm_paired_alignment RNASeqAlignment Reads 101487/308/1;101487/157/1 aligned to Genome 101487/2/1
JMB_tRNA_v2RNAseq_SampleSet_alignment_set ReadsAlignmentSet Set of all new alignments
Report
Summary
Created 33 alignments from the given alignment set.
Links
BW25113_Annotated
v1 - KBaseGenomes.Genome-9.0
The viewer for the data in this Cell is available at the original Narrative here: https://narrative.kbase.us/narrative/197146
Assemble Transcripts using StringTie - v2.1.5
Assemble the transcripts from RNA-seq read alignments using StringTie.
This app completed without errors in 5h 21m 49s.
Objects
Created Object Name Type Description
JMB_tRNA_v2RNAseq_SampleSet_expression_set ExpressionSet ExpressionSet generated by StringTie
truA_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
truA_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
truA_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
mnmC_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
mnmC_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
mnmC_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
mnmG_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
mnmG_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
mnmG_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
mnmA_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
mnmA_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
mnmA_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
thiI_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
thiI_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
thiI_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
rlmN_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
rlmN_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
rlmN_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
miaA_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
miaA_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
miaA_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
truD_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
truD_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
truD_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
dusB_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
dusB_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
dusB_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
trmJ_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
trmJ_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
trmJ_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
WT_R1_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
WT_R2_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
WT_R3_reads_trimm_paired_expression RNASeqExpression Expression generated by StringTie
JMB_tRNA_v2RNAseq_SampleSet_FPKM_ExpressionMatrix ExpressionMatrix FPKM ExpressionMatrix generated by StringTie
JMB_tRNA_v2RNAseq_SampleSet_TPM_ExpressionMatrix ExpressionMatrix TPM ExpressionMatrix generated by StringTie
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/197146
  • stringtie_result.zip - File(s) generated by StringTie App
Create Differential Expression Matrix using DESeq2 - v1.20.0
Create differential expression matrix based on a given threshold cutoff
This app completed without errors in 4h 22m 42s.
Objects
Created Object Name Type Description
JMB_tRNA_Total_DESeq2 DifferentialExpressionMatrixSet DifferentialExpressionMatrixSet generated by DESeq2
JMB_tRNA_Total_DESeq2-trmJ-VS-miaA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-miaA-VS-rlmN DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-dusB-VS-mnmC DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-WT-VS-mnmA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-miaA-VS-mnmG DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-dusB-VS-truA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-truD-VS-miaA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-WT-VS-mnmC DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-truD-VS-mnmC DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-dusB-VS-rlmN DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-mnmA-VS-mnmC DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-trmJ-VS-mnmG DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-trmJ-VS-dusB DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-dusB-VS-thiI DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-trmJ-VS-truA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-rlmN-VS-mnmG DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-WT-VS-truA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-dusB-VS-mnmA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-mnmA-VS-truA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-mnmG-VS-truA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-rlmN-VS-thiI DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-miaA-VS-mnmA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-thiI-VS-mnmA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-thiI-VS-truA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-thiI-VS-mnmC DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-miaA-VS-thiI DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-WT-VS-rlmN DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-dusB-VS-miaA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-mnmC-VS-truA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-trmJ-VS-mnmC DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-miaA-VS-truA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-WT-VS-dusB DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-rlmN-VS-mnmA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-WT-VS-thiI DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-truD-VS-mnmA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-mnmA-VS-mnmG DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-dusB-VS-truD DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-trmJ-VS-thiI DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-truD-VS-thiI DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-rlmN-VS-truA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-truD-VS-truA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-miaA-VS-mnmC DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-truD-VS-rlmN DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-rlmN-VS-mnmC DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-truD-VS-mnmG DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-WT-VS-mnmG DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-WT-VS-trmJ DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-WT-VS-truD DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-trmJ-VS-rlmN DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-thiI-VS-mnmG DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-WT-VS-miaA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-trmJ-VS-truD DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-dusB-VS-mnmG DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-mnmG-VS-mnmC DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
JMB_tRNA_Total_DESeq2-trmJ-VS-mnmA DifferentialExpressionMatrix DifferentialExpressionMatrix generated by DESeq2
Report
Links
Files
These are only available in the live Narrative: https://narrative.kbase.us/narrative/197146
  • DESeq2_result.zip - File(s) generated by DESeq2 App
  • DESeq2_plot.zip - Visualization plots by DESeq2 App

Filtered expression data to be used for downstream analyses

Expression matrices were created for each mutant versus WT and versus ∆dusB.

Data was filtered with alpha cutoff = 0.05 and Log2 fold change cutoff = 1.0

"Create Up/Down Regulated FeatureSet and ExpressionMatrix" tab has the overview report of how many genes (feature count) were up or down regulated in each comparison.

Create Up/Down Regulated FeatureSet and ExpressionMatrix
Create up/down regulated FeatureSet and ExpressionMatrix from differential expression data based on given cutoffs.
This app completed without errors in 10m 57s.
Objects
Created Object Name Type Description
JMB_tRNA_Total_DESeq2_WT-dusB_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_trmJ-dusB_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-miaA_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-miaA_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-mnmA_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-mnmA_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-mnmC_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-mnmC_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-mnmG_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-mnmG_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-rlmN_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-rlmN_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-thiI_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-thiI_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-trmJ_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-truA_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-truA_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-truD_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-truD_up_feature_set FeatureSet Upper FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-dusB_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_trmJ-dusB_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-miaA_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-miaA_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-mnmA_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-mnmA_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-mnmC_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-mnmC_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-mnmG_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-mnmG_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-rlmN_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-rlmN_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-thiI_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-thiI_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-trmJ_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-truA_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-truA_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_WT-truD_down_feature_set FeatureSet Lower FeatureSet Object
JMB_tRNA_Total_DESeq2_dusB-truD_down_feature_set FeatureSet Lower FeatureSet Object
WT-dusB_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
trmJ-dusB_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
dusB-miaA_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
WT-miaA_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
WT-mnmA_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
dusB-mnmA_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
WT-mnmC_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
dusB-mnmC_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
WT-mnmG_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
dusB-mnmG_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
WT-rlmN_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
dusB-rlmN_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
WT-thiI_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
dusB-thiI_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
WT-trmJ_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
WT-truA_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
dusB-truA_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
WT-truD_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
dusB-truD_filtered_expression_matrix ExpressionMatrix Filtered ExpressionMatrix Object
Report
Links 
from biokbase.narrative.jobs.appmanager import AppManager
AppManager().run_local_app(
    "NarrativeViewers/view_expression_interactive_heatmap",
    {
    "param0": "197146/565/4"
},
    tag="release",
    version="1.0.9",
    cell_id="dc5f69af-0149-4b30-8c4b-7590c94764fe",
    run_id="61b628c4-1d24-429d-b72a-c0cf4d8922ce"
)
Out[2]:

Apps

  1. Align Reads using HISAT2 - v2.1.0
    • Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nature Methods. 2015;12: 357 360. doi:10.1038/nmeth.3317
    • 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
  2. Assemble Transcripts using StringTie - v2.1.5
    • Frazee AC, Pertea G, Jaffe AE, Langmead B, Salzberg SL, Leek JT. Ballgown bridges the gap between transcriptome assembly and expression analysis. Nat Biotechnol. 2015;33: 243 246. doi:10.1038/nbt.3172
    • https://www.nature.com/articles/nmeth.3317
    • 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
    • Pertea M, Pertea GM, Antonescu CM, Chang T-C, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nature Biotechnology. 2015;33: 290 295. doi:10.1038/nbt.3122
    • 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. Assess Read Quality with FastQC - v0.12.1
    • FastQC source: Bioinformatics Group at the Babraham Institute, UK.
  4. 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
  5. Create RNA-seq SampleSet
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
  6. Create Up/Down Regulated FeatureSet and ExpressionMatrix
    • Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, et al. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nature Biotechnology. 2018;36: 566. doi: 10.1038/nbt.4163
  7. Trim Reads with Trimmomatic - v0.36
    • Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30: 2114 2120. doi:10.1093/bioinformatics/btu170