Entering edit mode
15 hours ago
Yvan
•
0
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
How about using https://genome.ucsc.edu/cgi-bin/hgPcr