On Wed, Feb 9, 2011 at 3:32 PM, Jennifer Jackson <j...@bx.psu.edu> wrote:
> Hi Peter,
>
> Sorry about that, I did a double check and you are right, the tool doesn't
> "screen" sequences. Maybe try BLAT itself to identify then clip? It depends
> on how long your primers are - shorter than 20 will need some tuning. Ask
> UCSC directly (Galt) about how to configure for this type of match:
> gen...@ucsc.edu.
>
> Best,
>
> Jen
> Galaxy team

Hi Jen,

Yes, my primer sequences are short - up to 22bp, so I don't think
BLAST is a good solution. I've been using regular expressions and
it seems to work nicely on my current 454 data (it would need testing
on some large datasets before I was happy it could be used on say
a full run of Illumina).

For the work in progress, see:
https://bitbucket.org/peterjc/galaxy-central/src/filter_fasta/tools/primers/

At the time of writing I have three tools, for FASTA, FASTQ and SFF
files. As per my recent email I am considering merging them into one
single tool:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2011-February/004294.html

Peter
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