I'm stuck in the middle of something. I have a selected gene list
(bed file) like this:
chr start end strand gene geneLength chr1 185217 195411 - ENSG00000279457 10194 chr1 725885 778626 - ENSG00000228327 52741 chr1 725885 778626 - ENSG00000228327 52741 chr1 916865 921016 - ENSG00000223764 4151 chr1 916865 921016 - ENSG00000223764 4151 chr1 916865 921016 - ENSG00000223764 4151 chr1 944204 959309 - ENSG00000188976 15105
I get them after different downstream analysis, and I need to calculate the read depth for them (only for those). So far, I've tried this:
genomeCoverageBed -ibam bam -g gene.list > coverage
But the output doesn't show the coverage for the specific gene.
and I also tried this:
bedtools coverage -a gene.list -b bam > coverage
but it gave me this error
***** WARNING: bam has inconsistent naming convention for record: GL000008.2 12857 12916 SRR6497147.21984058 0 - Killed
Any help? Thanks!!!