samtools coverage
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Entering edit mode
3 months ago
Candela • 0

Hi guys, I have mapped metagenomic sequencing reads to a collection of assembled sequences that represent several MAGs (previously binned from the metagenome sample) obtaining my bam file, and my idea is to get the average coverage values within 5 Kbp sliding windows sampled every 100 bp in each MAG draft genome. I found the function samtools depth that gives you depth of coverage per base pair, but anyone can tell me how to obtain the average coverage of the desire region that i want.

samtools bedtools coverage • 251 views
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Entering edit mode
3 months ago
yhoogstrate ▴ 110

I believe you can do that using the -b <bed> list of positions or regions argument and provide it a BED file with the regions of interest.