Question: BWA and mapping
gravatar for Juan Ledesma
4.8 years ago by
United Kingdom
Juan Ledesma0 wrote:

Hi everybody

I am Juan and I am very very new in this community. I am starting doing NGS data analysis and I have some doubts.

I using BWA to map my reads against a reference sequence. Afterwards I convert the sam file into a bam file that I can use to get a consensus sequence.My doubt is whether the sam/bam file I get after the mapping includes paired reads as well as the unpaired reads matching the reference sequence or only the paired reads and removes the reads as they don't have a mate. 

Thanks in advance



ADD COMMENTlink modified 4.8 years ago • written 4.8 years ago by Juan Ledesma0

Thanks for your help

ADD REPLYlink written 4.8 years ago by Juan Ledesma0
gravatar for Ashutosh Pandey
4.8 years ago by
Ashutosh Pandey12k wrote:

It will have both reads for a pair irrespective of whether one of them remained unmapped or mapped at too many positions. The second column in the BAM file will be properly flagged as explained here:

ADD COMMENTlink modified 8 months ago by RamRS28k • written 4.8 years ago by Ashutosh Pandey12k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1277 users visited in the last hour