Is it "bwa aln -q" a soft clip or hard clip?
I was wondering whether anyone could explain to me the following questions :
1. When using bwa for alignment, the "bwa aln " -q argument is doing a hard clipping on the sequence or soft? In another word, were the low quality base at 3' were clipped/excluded before alignment or just tagged as low quality? I want to make sure this won't cause problem for downstream de-duplication.
2. When transferring .sam to .bam later on, there's a choice to use "-q" to further filter the read with poor alignment quality. Do we need to do both "-q" at the alignment level and also after .sam ?
Thanks for your help!
Yan
1. When using bwa for alignment, the "bwa aln " -q argument is doing a hard clipping on the sequence or soft? In another word, were the low quality base at 3' were clipped/excluded before alignment or just tagged as low quality? I want to make sure this won't cause problem for downstream de-duplication.
2. When transferring .sam to .bam later on, there's a choice to use "-q" to further filter the read with poor alignment quality. Do we need to do both "-q" at the alignment level and also after .sam ?
Thanks for your help!
Yan