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7.5 years ago
sacha
★
2.4k
I have several primers in a fasta file (20nt). What's the best way to get genom coordinate of those primers ? Align with bwa ? Other tools ?
There has been a similar thread before with good suggestions: find positions of a short sequence in a genome
I have used blat . But bowtie also can do it. Never tried bwa for that.
Just ran :
let's see what is returning
You'll need to play with the parameters, in particular if you're also interested in positions with some mismatches. From the BLAT FAQ:
That's exactly what I noticed Do you know which parameters are used in BLAT web interface ? Because web interface returns me all alignement. default parameters of blat from console interface don't.
There is a section in the FAQ about replicating the web-based parameters with the command line tool and a section on using blat for short sequences. You could also use blastn instead with a window size of 6-8 and a high E-value threshold.