pileup crashing
changing project name
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...
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...