Question: Contig's coverage and bam files.
gravatar for Picasa
4.2 years ago by
Picasa590 wrote:


I would like to compute the contig coverage I got from an assembly.

I have different lib (of insert size) so i've mapped it separately, at the end I have a .bam file for each library:


Now I would like to give it to BBmap for coverage computation.

But I think I have to merge the 2.bam files with :

samtools merge output.bam *.bam

I'm not sure, Is it the right way to do ?

bam coverage contig • 1.4k views
ADD COMMENTlink modified 4.0 years ago by Biostar ♦♦ 20 • written 4.2 years ago by Picasa590

Yes, If you need to how many of your reads are used probably in the assembly, so If you have less coverage that would mean you have something went wrong, you need to put in your mind that after merging if you have 1X before it should be 2X for each region "just an estimation"

ADD REPLYlink modified 4.2 years ago • written 4.2 years ago by Medhat8.8k

Should I remove duplicates reads ?

ADD REPLYlink written 4.2 years ago by Picasa590

Did you removed it first before running the assembly ? cause you should remove PCR and optical duplicate

ADD REPLYlink written 4.2 years ago by Medhat8.8k
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