From 87e9a9b56f16963e01ec53f86c1cda9837fd08bb Mon Sep 17 00:00:00 2001 From: Barbara Novak <19824106+bnovak32@users.noreply.github.com> Date: Mon, 18 Aug 2025 09:45:37 -0700 Subject: [PATCH 1/3] Added assay suffix for remaining output files GL-DPPD-7101-G --- .../GL-DPPD-7101-G.md | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md b/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md index 443452c7f..4beea3719 100644 --- a/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md +++ b/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md @@ -277,7 +277,7 @@ trim_galore --gzip \ **Output Data:** -- **\*fastq.gz** (trimmed reads) +- **\*\_GLbulkRNAseq{_R1,_R2}_trimmed_fastq.gz** (trimmed reads) - **\*trimming_report.txt** (trimming report)
@@ -462,8 +462,8 @@ gzip *_unmapped.fastq **Output Data:** - *Aligned.sortedByCoord.out.bam (sorted mapping to genome) -- **\*Aligned.toTranscriptome.out.bam** (sorted mapping to transcriptome) -- **\*Log.final.out** (log file containing alignment info/stats such as reads mapped, etc) +- **\*_GLbulkRNAseq_Aligned.toTranscriptome.out.bam** (sorted mapping to transcriptome) +- **\*_GLbulkRNAseq_Log.final.out** (log file containing alignment info/stats such as reads mapped, etc) - *ReadsPerGene.out.tab (tab delimitated file containing STAR read counts per gene with 4 columns that correspond to different strandedness options: column 1 = gene ID, column 2 = counts for unstranded RNAseq, column 3 = counts for 1st read strand aligned with RNA, column 4 = counts for 2nd read strand aligned with RNA) - *Log.out (main log file containing detailed info about the STAR run) - *Log.progress.out (minute-by-minute report containing job progress statistics, such as the number of processed reads, % of mapped reads etc.) @@ -476,7 +476,7 @@ gzip *_unmapped.fastq - SJ.out.tab - *_STARtmp (directory containing the following:) - BAMsort (directory containing subdirectories that are empty – this was the location for temp files that were automatically removed after successful completion) -- **\*unmapped.fastq.gz** (unmapped and partially mapped reads) +- **\*\_GLbulkRNAseq{_R1,_R2}_unmapped.fastq.gz** (unmapped and partially mapped reads)
@@ -580,7 +580,7 @@ samtools sort -m 3G \ **Output Data:** -- **\*Aligned.sortedByCoord_sorted.out.bam** (samtools sorted genome aligned bam file) +- **\*_GLbulkRNAseq_Aligned.sortedByCoord_sorted.out.bam** (samtools sorted genome aligned bam file)
@@ -601,7 +601,7 @@ samtools index -@ NumberOfThreads /path/to/*Aligned.sortedByCoord_sorted.out.bam **Output Data:** -- **\*Aligned.sortedByCoord_sorted.out.bam.bai** (index of sorted mapping to genome file) +- **\*_GLbulkRNAseq_Aligned.sortedByCoord_sorted.out.bam.bai** (index of sorted mapping to genome file)
@@ -966,8 +966,8 @@ rsem-calculate-expression --num-threads NumberOfThreads \ **Output Data:** -- **\*genes.results** (counts per gene) -- **\*isoforms.results** (counts per isoform) +- **\*_GLbulkRNAseq.genes.results** (counts per gene) +- **\*_GLbulkRNAseq.isoforms.results** (counts per isoform) - *stat (directory containing the following stats files) - *cnt - *model @@ -1093,7 +1093,7 @@ echo "*: ${rRNA_count} rRNA entries removed." > *_rRNA_counts.txt - *rrna_ensembl_ids.txt (file containing list of gene IDs with rRNA features, output from [Step 8di](#8di-extract-rrna-gene-ids-from-gtf)) **Output Data:** -- **\*rRNArm.genes.results** (RSEM gene counts with rRNA entries removed) +- **\*_GLbulkRNAseq_rRNArm.genes.results** (RSEM gene counts with rRNA entries removed) - *rRNA_counts.txt (Summary of number of rRNA entries removed)
From 1ac9afad4fb4638864a4f547eecec3cde5a16acd Mon Sep 17 00:00:00 2001 From: Barbara Novak <19824106+bnovak32@users.noreply.github.com> Date: Tue, 19 Aug 2025 13:44:41 -0700 Subject: [PATCH 2/3] added assay suffixes to RNAseq microbe pipeline --- RNAseq/Pipeline_GL-DPPD-7115_Versions/GL-DPPD-7115.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/RNAseq/Pipeline_GL-DPPD-7115_Versions/GL-DPPD-7115.md b/RNAseq/Pipeline_GL-DPPD-7115_Versions/GL-DPPD-7115.md index a60207d71..8a2e4eefe 100644 --- a/RNAseq/Pipeline_GL-DPPD-7115_Versions/GL-DPPD-7115.md +++ b/RNAseq/Pipeline_GL-DPPD-7115_Versions/GL-DPPD-7115.md @@ -216,7 +216,7 @@ trim_galore --gzip \ **Output Data:** -- **\*fastq.gz** (trimmed reads) +- **\*\_GLbulkRNAseq{_R1,_R2}_trimmed_fastq.gz** (trimmed reads) - **\*trimming_report.txt** (trimming report)
@@ -356,8 +356,8 @@ mv .unmapped.fastq.2.gz _R2_unmapped.fastq.gz # For paire **Output Data:** - *\.sam (alignments in SAM format) -- **\*.bowtie2.log** (log file containing alignment statistics) -- **\*unmapped.fastq.gz** (unmapped and partially mapped reads) +- **\*_GLbulkRNAseq.bowtie2.log** (log file containing alignment statistics) +- **\*_GLbulkRNAseq{_R1,_R2}_unmapped.fastq.gz** (unmapped and partially mapped reads)
@@ -435,7 +435,7 @@ samtools sort -m 3G \ **Output Data:** -- **\*_sorted.bam** (samtools sorted genome-aligned bam file) +- **\*_GLbulkRNAseq_sorted.bam** (samtools sorted genome-aligned bam file)
@@ -456,7 +456,7 @@ samtools index -@ NumberOfThreads /path/to/*_sorted.bam **Output Data:** -- **\*_sorted.bam.bai** (index of sorted mapping to genome file) +- **\*_GLbulkRNAseq_sorted.bam.bai** (index of sorted mapping to genome file)
From 69d6889ef113d09be77aa5b7e3b4e9957101e5df Mon Sep 17 00:00:00 2001 From: Barbara Novak <19824106+bnovak32@users.noreply.github.com> Date: Tue, 19 Aug 2025 16:27:59 -0700 Subject: [PATCH 3/3] added suffix for SJ.out.tab file in eukaryotic pipeline --- RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md b/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md index 4beea3719..199810bc2 100644 --- a/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md +++ b/RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md @@ -467,7 +467,7 @@ gzip *_unmapped.fastq - *ReadsPerGene.out.tab (tab delimitated file containing STAR read counts per gene with 4 columns that correspond to different strandedness options: column 1 = gene ID, column 2 = counts for unstranded RNAseq, column 3 = counts for 1st read strand aligned with RNA, column 4 = counts for 2nd read strand aligned with RNA) - *Log.out (main log file containing detailed info about the STAR run) - *Log.progress.out (minute-by-minute report containing job progress statistics, such as the number of processed reads, % of mapped reads etc.) -- **\*SJ.out.tab** (high confidence collapsed splice junctions in tab-delimited format) +- **\*_GLbulkRNAseq_SJ.out.tab** (high confidence collapsed splice junctions in tab-delimited format) - *_STARgenome (directory containing the following:) - sjdbInfo.txt - sjdbList.out.tab