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Merged
bnovak32 merged 3 commits into from
Aug 20, 2025
Merged

RNAseq add assay suffixes #173

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87e9a9b
Added assay suffix for remaining output files GL-DPPD-7101-G
bnovak32 Aug 18, 2025
1ac9afa
added assay suffixes to RNAseq microbe pipeline
bnovak32 Aug 19, 2025
69d6889
added suffix for SJ.out.tab file in eukaryotic pipeline
bnovak32 Aug 19, 2025
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20 changes: 10 additions & 10 deletions RNAseq/Pipeline_GL-DPPD-7101_Versions/GL-DPPD-7101-G.md
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Expand Up @@ -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)

<br>
Expand Down Expand Up @@ -462,12 +462,12 @@ 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.)
- **\*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
Expand All @@ -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)

<br>

Expand Down Expand Up @@ -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)

<br>

Expand All @@ -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)

<br>

Expand Down Expand Up @@ -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
Expand Down Expand Up @@ -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)

<br>
Expand Down
10 changes: 5 additions & 5 deletions RNAseq/Pipeline_GL-DPPD-7115_Versions/GL-DPPD-7115.md
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Expand Up @@ -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)

<br>
Expand Down Expand Up @@ -356,8 +356,8 @@ mv <sample_id>.unmapped.fastq.2.gz <sample_id>_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)

<br>

Expand Down Expand Up @@ -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)

<br>

Expand All @@ -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)

<br>

Expand Down
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