Gene coverage detection output from pileup.sh

BBMap short read aligner, and other bioinformatic tools.

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Gene coverage detection output from pileup.sh

Forum: General Discussion

Creator: Linton Freund

Created: 2021-12-20

Updated: 2021-12-20

Linton Freund - 2021-12-20

I am currently using pileup.sh to determine the coverage of genes in my metagenomes by comparing my read mapping alignment file to the gene predictions of the contigs identified by Prodigal. I was wondering if anyone could tell me the output for the gene_coverage.tmp file, and if there are the same headers as the contig_comverage.tmp files? I am not sure if I should use the avgDepth value or the depthSum for my coverage value when I go to normalize these counts to counts per million (CPM).

I am adding a screenshot that shows the column headers in this gene_coverage tmp file. Thanks for your help and for making such a great set of tools!

Screen Shot 2021-12-20 at 9.02.21 AM.png

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