Hi All,
I have a bed file called my_region.bed
as below:
Ch1 0 3951982 my_region 0 +
Ch2 0 3683506 my_region 0 +
Ch3 0 3351453 my_region 0 +
Ch4 0 2873318 my_region 0 +
Ch5 0 2822964 my_region 0 +
Ch6 0 2483831 my_region 0 +
Ch7 0 2434682 my_region 0 +
Ch8 0 2299506 my_region 0 +
Ch9 0 2122865 my_region 0 +
Ch10 0 2105496 my_region 0 +
Ch11 0 2052242 my_region 0 +
Ch12 0 1878461 my_region 0 +
Ch13 0 1845946 my_region 0 +
Ch14 0 1815632 my_region 0 +
Ch15 0 1765292 my_region 0 +
Ch16 0 1419421 my_region 0 +
I tried to extract the coverage for each nucleotide position on these chromosomes from my bam file using these commands: for positive strand,
bedtools coverage -a my_region.bed -b file.bam -bed -d -s | gzip > coverage_positive.tsv.gz
and for negative strand
bedtools coverage -a my_region.bed -b file.bam -bed -d -S | gzip > coverage_negative.tsv.gz
However, these commands only give me positions expaning all chromosomes without their actual coverage (everything is zero in coverage column). Also, these commands work perfectly fine when I have only one chromosome on my bed file, but doesn't seem to work if I have all chromosomes as shown above. Could someone please let me know what I need to do instead of these commands. Thanks!
mosdepth
(https://github.com/brentp/mosdepth ) is recommended for this application.Thanks, but couldn't make this work on individual base positions.
What does your bed file look like? Did you try making the bed regions 1 bp in length, if you only have one bp locations?
generates
That's the default...