Mapping PCR primers to human genome
Hello,
I have around 5000 primers pairs that I need to map against the human genome. So far I am using a two steps approach, creating an index file then mapping these indexes against the reference
bwa aln -o 0 -n 1 ref.fasta primers.fasta > primers.fai
bwa samse ref.fasta primers.fai primers.fasta > primers.sam
I am using these options:
-o set to zero to avoid gap opening.
-n set to 1 for only one mismatch
Does anyone have this kind of problem, or anyone have a better solution? Different type of mapper? Dragen? Blast?
Thanks for your help
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How about using https://genome.ucsc.edu/cgi-bin/hgPcr
Thanks for the pointer , but I have more than 6000 primer pairs.
That likely uses
blat(another tool written by Jim Kent). As long as you are an academic user you can downloadblatlocally and run it. You could also run a program calledgfserver(if you have the right hardware available). You can read about both tools here: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/Super, thanks, I will try.