Question: BWA or SMALT mapping algorithm
gravatar for P.NJ
5.8 years ago by
P.NJ50 wrote:

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 ?

bwa illumina reads 2x250bp smalt • 2.5k views
ADD COMMENTlink modified 5.8 years ago • written 5.8 years ago by P.NJ50

Could you please describe "'gene-pooled' exonic gene regions " in more detail?

ADD REPLYlink written 5.8 years ago by Biomonika (Noolean)3.1k

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 ?

ADD REPLYlink written 5.8 years ago by P.NJ50

bwa-aln does not work well for 250bp reads.

ADD REPLYlink written 5.8 years ago by lh332k

what would be an alternative then ?

ADD REPLYlink written 5.8 years ago by P.NJ50

I probably would say bwa mem?

ADD REPLYlink written 5.7 years ago by 141341254653464453.5k
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