I am currently mapping read from different read length (from 30 to 100) and I have been using BWA-mem and BWA-aln. I know that BWA-aln works better for those read's length but while I was analysing my bam files I realised that every reads < 35bp are set as "unmapped" by BWA-mem. So here is my question:
Does the reads shorter than 35bp does not map because BWA-mem is not optimised for those reads ? If yes, why why some of 37-39 would map? (I have around 50K reads < 35bp and 100K < 40bp)
Is there, somewhere in the code, a limit of read length where BWA-mem doesn't even try to align the reads ? Would be good to find a proof in the code but didn't find anything about that in the code (https://github.com/lh3/bwa). My C skills are not the best tho' so I might have missed it.
Thanks a lot !