Fastq Format Problem When Using Bwa Aln -Q Option (Read Trim)

Question

[Bioscientist]

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?

Thanks

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?

Answer 1

[Damian Kao]

Here is a good thread on seqanswers about converting Illumina to Sanger quality scores.

Here is a good description of what the quality scores are: http://en.wikipedia.org/wiki/FASTQ_format#Quality