Weird alignments in amplicon sequencing
0
0
Entering edit mode
8.1 years ago
kulvait ▴ 270

Hi, we are using Illumina Myeloid panel of ~500 amplicons to sequence certain part of exome by Illumina HiSeq. I were doing alignment using bwa mem with default parameters. In some regions the quality of mapping is very poor. In the first case Lot of mismatches there is lot of mismatches and in the second case Lot of softclippingthere is lot of soft clipping or mismatches at the ends of some reads. Is it possible to somehow force bwa mem to discard these mappings and is it wise? I mean would you set some speciffic parameters to bwa mem mapping to avoid these or are these virtually unavoidable?

Thanks Vojtech.

amplicon-seq sequencing myeloid • 1.9k views
ADD COMMENT
0
Entering edit mode

Hi, what aligner do you use? You could try to increase in bwa-mem parameter B - penalty for mismatch and -L penalty for 5' and 3' end clipping.

ADD REPLY
0
Entering edit mode

I have been using bwa mem with default parameters. This problem affects minority of the data. Thank you for recomendation, do you have experience with particular setting, we will consider using that.

ADD REPLY

Login before adding your answer.

Traffic: 1973 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6