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Old 09-11-2009, 02:15 AM   #1
Junior Member
Location: London

Join Date: Jan 2009
Posts: 8
Default Removing an unknown primer sequence from reads.


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, 04:42 AM   #2
Jose Blanca
Location: Valencia, Spain

Join Date: Aug 2009
Posts: 70

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 script.
If you're interested write me an email (jblanca _at_
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Old 09-12-2009, 10:57 PM   #3
Location: San Francisco

Join Date: Sep 2009
Posts: 44

Take a look at Figaro (
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