Question: Get coordinate of several primer fasta sequence
0
gravatar for sacha
2.1 years ago by
sacha1.7k
France
sacha1.7k wrote:

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 ?

ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by sacha1.7k
1

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

ADD REPLYlink written 2.1 years ago by WouterDeCoster38k

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

ADD REPLYlink written 2.1 years ago by microfuge1.0k

Just ran :

  blat hg19.fa amorce_forward.fa forward.psl

let's see what is returning

ADD REPLYlink written 2.1 years ago by sacha1.7k

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.)

ADD REPLYlink modified 2.1 years ago • written 2.1 years ago by Jean-Karim Heriche18k

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.

ADD REPLYlink written 2.1 years ago by sacha1.7k

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.

ADD REPLYlink written 2.1 years ago by Jean-Karim Heriche18k
0
gravatar for sacha
2.1 years ago by
sacha1.7k
France
sacha1.7k wrote:

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

ADD COMMENTlink written 2.1 years ago by sacha1.7k
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