Entering edit mode
10.5 years ago
P.NJ
▴
50
I am using BWA for aligning targeted 'gene-pooled' exonic gene regions generated from Illumina 1.9 against whole genome human reference. The parameters I used for the command "aln" are
bwa aln -n 2 -q 15 -l 35 -t 8 -I
But I was just wondering if it is a good idea to disable the seeding and also change -n to 0.01 ? Also, my sequencing data is Illumina paired-end data (2x250 bp). So will other algorithms such bwa-mem or SMALT be better to use than bwa-aln?
Could you please describe "'gene-pooled' exonic gene regions" in more detail?
To explain it in simple words, DNA samples from cases and controls are combined together to form a population library and processed to produce sequence data for the defined target regions in the genes...
Any suggestions for my questions?
bwa-aln does not work well for 250bp reads.
what would be an alternative then ?
I probably would say bwa mem?