Get coordinate of several primer fasta sequence

Question

[sacha]

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 ?

[WouterDeCoster]

There has been a similar thread before with good suggestions: find positions of a short sequence in a genome

[microfuge]

I have used blat . But bowtie also can do it. Never tried bwa for that.

[sacha]

Just ran :

  blat hg19.fa amorce_forward.fa forward.psl

let's see what is returning

[Jean-Karim Heriche]

You'll need to play with the parameters, in particular if you're also interested in positions with some mismatches. From the BLAT FAQ:

Blat of DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more. It may miss more divergent or shorter sequence alignments. (The default settings and expected behavior of standalone Blat are slightly different from those on the graphical version of Blat.)

[sacha]

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.

[Jean-Karim Heriche]

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.

Answer 1

[sacha]

So I did it with bowtie2 . And it works perfectly . But I need to generate an index. Blat doesn't need it. https://github.com/dridk/primersnp