BWA MEM anfter trimming

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3.0 years ago

Edmond • 0

Hi there,

I have WES data. The read length is 35-101 bp. If I trim the sequence, I get 15-70 length sequence. I trimmed based and performed illumicaclip order on trimmomatic.

The question is as follows:

I should get a mean coverage of X100, (based on the analysis of the same fastq files). However I get 68X of coverage.

I think it could be related with the aligner: Mi idea is that when I perform the alignment on the trimmed data, I use BWA-MEM however is on the limit of the minimum read length. Should I modify the default parameters?

Because the Quality of the alignment according to qualimap is 40. I think this is a low BQ.

The per base sequence plot before and after are here:

enter image description here

BWA Alignment MEM • 1.0k views

ADD COMMENT • link 3.0 years ago by Edmond • 0

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Don't trim the initial base pairs as you are throwing away good data. See: https://sequencing.qcfail.com/articles/positional-sequence-bias-in-random-primed-libraries/ This is also true for tagmented libraries.