Hi everyone, I'm trying to use "mosdepth" in order to get the depth in each position in a bam file i have (of rna-seq data). I tried to run -
mosdepth output_file bam_file
and one of the files i get is:
When I open this file i see that actually the depth i get is not always per position, but most of the times it is for some preceding positions:
- 1 18500 18505 8
- 1 18505 18514 7
- 1 18514 18517 6
- 1 18517 18519 5
and so on...
Because i need the positions with depth >= 2, i'm not sure how i can use this output.
btw, i tried to use --thresholds 2, but it didn't work...
Thanks in advance