What is the best way to compute scaffold coverage ?

Question

[Picasa]

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.

[Picasa]

Nobody got an answer ?

[GenoMax]

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.

[Picasa]

I'll try but I would like whether there are people doing that kind of things and if the method is good.