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: