BWA trim doesn’t work.

[CNVboy]

I tried to run BWA with trimming those low-quality bases around the end of read. And command is like:

/share/bin/bwa aln -t 7 -I -q 20 ****.txt.gz > ****.sai

Here -I is to convert Illumina format to sanger
However when I check the generated sam file, I can still see lines like:

HWI-ST150_0131:3:1:5473:1943#0  133 X   113713314   0   35M5S   =   113713314   0   TNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN    ########################################    XC:i:35

Shouldn't the crappy sequences trimmed? Or my command has some problems?thx

[cjp]

In here for 133 - the samtools flags: http://picard.sourceforge.net/explain-flags.html

you get:

Summary:
read paired
read unmapped
second in pair

So the read is unmapped:

Also see this thread from today about bwa-mapped reads with the unmapped flag:

http://seqanswers.com/forums/showthread.php?t=15772

Chris