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-   -   Removing an unknown primer sequence from reads. (http://seqanswers.com/forums/showthread.php?t=2565)

mchotalia 09-11-2009 02:15 AM

Removing an unknown primer sequence from reads.
 
Hi,

Could anyone help me learn how to remove an unknown primer sequence from the ends of reads. I have these primers attached to the DNA prior to making the Illumina libraries as i have used them for other reactions. This means that when the data is compiled i have a lot of data that is unmappable due to these primers.

Any ideas?

I have to admit...i'm no bioinformatician so could you keep your replies easy for me to understand please.

Thanks in advance

Jose Blanca 09-11-2009 04:42 AM

We have develop a tool to clean different kind of sequences. It can remove adaptor sequences from solexa reads. We haven't write the documentation yet. You can take a look at the biolib project code.
To clean the sequences we use the run_cleanning_pipeline.py script.
If you're interested write me an email (jblanca _at_ btc.upv.es).

spenthil 09-12-2009 10:57 PM

Take a look at Figaro (http://sourceforge.net/apps/mediawik...p?title=Figaro).


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