Mapping PCR primers to human genome

Question

[Yvan]

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

1. bwa aln -o 0 -n 1 ref.fasta primers.fasta > primers.fai

2. 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

[GenoMax]

How about using https://genome.ucsc.edu/cgi-bin/hgPcr

[Yvan]

Thanks for the pointer , but I have more than 6000 primer pairs.

[GenoMax]

That likely uses blat (another tool written by Jim Kent). As long as you are an academic user you can download blat locally and run it. You could also run a program called gfserver (if you have the right hardware available). You can read about both tools here: http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/

[Yvan]

Super, thanks, I will try.