What is the best way to compute scaffold coverage ?
So I have different type of data composed of paired end and single reads (Let's say 2 PE and 1 SE)
I want the coverage for each scaffold and a general coverage (so for this one I want a number like 50X), my idea is :
1) Map my datas on the scaffold: So at the end, I have 3 .bam file.
2) Using samtools to merge my bam:
samtools merge merged.bam in.1.bam in.2.bam ...
3) And finally using, genomecov from BEDtools:
http://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
Is it consistent or there is a best way to do that ??
Thanks.
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Nobody got an answer ?
Why not try doing it the way you proposed to above? If you just need broad coverage numbers you could use Qualimap on the merged bam file.
I'll try but I would like whether there are people doing that kind of things and if the method is good.