Question: Does BWA (BWA-MEM) care about the identity and coverage of the mapped reads?
0
gravatar for culiu
15 months ago by
culiu0
culiu0 wrote:

Hi All,

I am planning to jump from one old alignment method to BWA-MEM to analyse my 300 bp PE Illumina reads.

The old alignment method can filter the alignment result by identity and coverage of the mapped/aligned reads.

But in BWA-MEM, neither seems to have been mentioned.

Is it reasonable that the BWA-MEM can do split alignment and reduce the reference bias so it does not care about the relationships between the reads and the reference???

ADD COMMENTlink modified 15 months ago by shaun80 • written 15 months ago by culiu0
0
gravatar for shaun
15 months ago by
shaun80
Israel
shaun80 wrote:

You can tweak these features with the -B (mismatch penalty) -O and -E (gap penalties). You can see the coverage and mismatches in the resulting bam file and post-process it if you think the results are unsatisfying using samtools for instance.

ADD COMMENTlink written 15 months ago by shaun80

Thanks for the reply, EvoBI!!

Yea. I also thought of this idea. But I still cannot go back to the exact settings (e.g., mapping identity = 90%, read coverage = 90%), right?

ADD REPLYlink written 15 months ago by culiu0

I wondered about that before as well, but ended up with the method @EvoBl mentioned. The accurate coverage won't be unveiled till after alignment anyway.

ADD REPLYlink written 15 months ago by Helene390
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