Contig's coverage and bam files.

Question

[Picasa]

Hi,

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:

insert_size_350.bam
insert_size_550.bam

Now I would like to give it to BBmap pileup.sh 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 ?

[Medhat]

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"

[Picasa]

Should I remove duplicates reads ?

[Medhat]

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