I tried to run BWA with trimming those low-quality bases around the end of read. And command is like:
Here -I is to convert Illumina format to sanger
However when I check the generated sam file, I can still see lines like:
Shouldn't the crappy sequences trimmed? Or my command has some problems?thx
Code:
/share/bin/bwa aln -t 7 -I -q 20 ****.txt.gz > ****.sai
However when I check the generated sam file, I can still see lines like:
Code:
HWI-ST150_0131:3:1:5473:1943#0 133 X 113713314 0 35M5S = 113713314 0 TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN ######################################## XC:i:35
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