Hi Peter -

Regular expressions are a great, simple, and often fast solution to cleaning up seqs - glad that it is working for you. I am sure others will be interested in your tools, too, once you have them ready for the Tool Shed.

Thanks for all of your contributions to Galaxy!


On 2/9/11 7:42 AM, Peter Cock wrote:
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:


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:

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:


Jennifer Jackson
galaxy-dev mailing list

Reply via email to