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Hi all,
I used bwa mem to align my quality trimmed reads to a reference. I have 5M reads to align but in the sam file there are only 3M of them included (I grep the read names' initial part and count).
There is the "4" flag for many of the reads that are present in the sam file as unaligned. So I do not understand where the rest of the reads are. Does bwamem has a preference for which reads to align and report? Any ideas on this?
bwa mem index reads.fastq > align.sam
Thank y'all!
Melis
I used bwa mem to align my quality trimmed reads to a reference. I have 5M reads to align but in the sam file there are only 3M of them included (I grep the read names' initial part and count).
There is the "4" flag for many of the reads that are present in the sam file as unaligned. So I do not understand where the rest of the reads are. Does bwamem has a preference for which reads to align and report? Any ideas on this?
bwa mem index reads.fastq > align.sam
Thank y'all!
Melis