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RNAseq workflow using snakemake
Currently Loaded Modules:
module load gbc-samtools/1.12 gbc-hisat2/2.2.1 gbc-cutadapt/1.16 python/py37-anaconda-2019.10 snakemake/5.7.1-py37 gbc-fastqc gbc-subread
Step-by-step of i
Code Snippets
26 27 28 | run: for sample in sample_ids: print("Wrapping up pipeline") |
34 | shell: "mkdir -p {params.dirs}" |
50 | shell: "cutadapt -m 15 -a {params.adapter1} -A {params.adapter2} -n 2 -o {output.trimmed_read1} -p {output.trimmed_read2} {input.all_read1} {input.all_read2} >{output.trimmed_stats}" |
60 | shell: "fastqc {input.read1} -o outputs/fastqc ; fastqc {input.read2} -q -o outputs/fastqc/" |
76 77 78 79 | shell: """ hisat2 --threads {params.thread} -1 {input.p1} -2 {input.p2} -x {params.reference} 2> {output.stats} | samtools sort -T {output.mapped_bam_file}.tmp -O bam -o {output.mapped_bam_file} """ |
87 | shell: "samtools view -hb {input.sorted_bam} | samtools sort -T {input.sorted_bam}.tmp -o {output.sorted_bam_file}" |
95 | shell: "samtools index {input.index_bam} {output.index_bam_file}" |
104 | shell: "featureCounts -a /projects/academic/gbcstaff/igenome-041714/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf -o {output.counts_file} -T 6 /projects/academic/gbcstaff/Intern_Projects/achisha/RNAseq_test/outputs/sorted/*.sorted.bam" |
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Created: 1yr ago
Updated: 1yr ago
Maitainers:
public
URL:
https://github.com/UBGBC/RNAseq
Name:
rnaseq
Version:
4
Downloaded:
0
Copyright:
Public Domain
License:
None
- Future updates
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