I see that BWA ALN has an "-I" flag for changing the quality of the reads. I don't see this option for BWA MEM? Does anyone know if I'm missing something?
You're not missing anything: Bwa Mem: How To Specify The Fastq Phred Format? (see my link to a bwa email list message about this from Heng Li).
what is the size of your reads ? See Heng's comment:Aligning Sequence Reads, Clone Sequences And Assembly Contigs With Bwa-Mem
BWA-MEM however lacks the following features:
100bp. I wanted to use mem for consistency across some simulations and real data.
Honestly, I was stuck between mem and aln for my 100bp data, and aln performed much better, more reads aligned.
You can use my reformat tool to change ASCII-64 qualities to ASCII-33 (and most other format conversions). It supports piping from stdin and to stdout, so you don't have to write a temp file. And it's the fastest format convert of which I am aware.
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