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Old 09-11-2009, 03:15 AM   #1
mchotalia
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Location: London

Join Date: Jan 2009
Posts: 8
Default 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
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Old 09-11-2009, 05:42 AM   #2
Jose Blanca
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Location: Valencia, Spain

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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).
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Old 09-12-2009, 11:57 PM   #3
spenthil
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Take a look at Figaro (http://sourceforge.net/apps/mediawik...p?title=Figaro).
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