This is kind of follow-up question of http://biostar.stackexchange.com/questions/14723/trim-the-low-quality-end-of-100bp-read
My paired-end reads are 100bp, and in Illumina 1.5+ format. Now I need to run like:
bwa aln -q 20
I'm just wondering do I need to first convert Illumina 1.5+ format to Sanger format? Or simply set
-q 46 ? (Since Sanger format is phred+33; while Ilumina 1.5+ is phred+64)
Actually I'm a little bit confused about Sanger, Illumina 1.3, Illumina 1.5. What are these? Where do they come from?
Edit: I just notice bwa aln has an "I" option, which converts Illumina 1.3 to sanger. But what about Illumina 1.5? Can it be applied to 1.5?