Hi All,
I'm using fastq screen to check some files. It runs fine, but I noticed that when using bwa as aligner it defaults to bwa mem, as mentioned in the docs for the --aligner parameter
... BWA with mem -a
As I have 42bp SE reads I'd rather use bwa aln, which isn't mentioned anywhere in the docs, so I was wondering if there's a way to hack this default and instruct fastq screen to use aln and not mem. I tried to play with the parameter
bwa "<"text">" : Specify extra parameters to be passed to BWA
but I don't seem to get an acceptable syntax.
Does anyone know whether this
1) is possible at all
2) if yes, how to do it?
That's not a bad idea, i'll give it a shot, thanks! Any clue if the .sai file produced by aln would be enough or if I need to wrap samse/sampe as well?
Are you not seeing expected results? Since
fastq screen
is a quality check (and not serious analysis) you may be ok with thebwa
default.I'm using the --tag --filter parameters to select reads based on alignment on multiple genomes, which I will next map for "serious analysis". It has to map all the files (without subsetting) to multiple genomes and mem is slower than aln for short reads, it's taking ages.
It is rather to optimize the poipeline for the next time I run it rather than for a serious issue with the result
Are you looking to bin the reads subsequently? If you know the genomes you are interested in I suggest you use
bbsplit.sh
from BBMap suite to do this job once. No need for multiple passes.you'll need same/sampe