master-noddy / master-noddy/data-analysis
Get mean coverage of all genes present in Homo_sapiens.GRCh37.87.gtf from list of sample patients
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Description
while read sample; do while read gene; do grep -w "$gene" Homo_sapiens.GRCh37.87.gtf | awk '{if($2=="ensembl_havana" && $3=="CDS") print "chr"$1"\t"$4"\t"$5}' | bedtools intersect -a - -b Truseq_45MB_bed.wo_chrM.bed | bedtools coverage -b "$sample" -a - -d | awk '{print $1"\t"($2+$4-1)"\t"$5}' | sort | uniq | cut -f3 | Rscript -e 'mean(as.numeric(readLines("stdin")))' | awk '{print "'$sample'""\t""'$gene'""\t"$2}' >> result_file; done < gene_list_for_coverage.txt; done < sample_list
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with the command in the issue and inspect gene_list_for_coverage.txt, sample_list, Homo_sapiens.GRCh37.87.gtf, and Truseq_45MB_bed.wo_chrM.bed. Run it against the listed sample files and verify that result_file contains one mean-coverage value for each sample and gene combination.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r, shell
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100