I want to get per nucleotide coverage for my particular gene (geneX) which I added in the fasta file. There are other chromosomes present in the bam file, whose per nu coverage I am not interested in. When I use genomeCoverageBed tool to calculate per nucleotide coverage for my gene I also get coverage for other chromosomes which should not be the case if you look at my command below
samtools view -bh test.bam geneX | genomeCoverageBed - ibam stdin -g my.genome -d > out.txt
my my.genome looks like this
This runs for a very long time because the program still looks for chr1, chr2 etc??
Anyway I can only get per nuc counts for geneX.