Question: BLASR: How to subsample alignments from a region
0
gravatar for shwethacm
3.3 years ago by
shwethacm200
Seattle, WA
shwethacm200 wrote:

Hello! 

I have an alignment of ~20x PacBio long reads to my reference genome and I am trying to extract alignments within only a certain region, say 2mb-10mb (sort of like samtools view ) but I am not sure how to do this.

I have alignments in the m4 format.

I think I should be specifying a region table but I am not sure.

Can anybody help?  

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by shwethacm200
0
gravatar for rhall
3.3 years ago by
rhall160
United States
rhall160 wrote:

I'm not aware of any software to process m4 files, but they are straightforward to parse with simple scripts, https://github.com/PacificBiosciences/blasr/wiki/Blasr-Output-Format . If you are more comfortable with sam format, blasr can output sam instead of m4, the '-sam' parameter.

 

ADD COMMENTlink written 3.3 years ago by rhall160
0
gravatar for shwethacm
3.3 years ago by
shwethacm200
Seattle, WA
shwethacm200 wrote:

Thanks, rhall. 

I did eventually parse it myself but I was looking to check if I could be lazy about it and do it quickly using a preexisting tool :)  

Well, now I know! 

Thanks a ton anyway. 

Shwetha 

ADD COMMENTlink written 3.3 years ago by shwethacm200
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