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Old 01-04-2011, 04:44 AM   #1
agc
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Default Extracting reads with specific barcodes

Hi,

I've received Illumina PE files, which I've been told contain several samples, and that the barcode I want is GT. From what I've understood, barcodes are a sequence of 2-3 bases added to the beginning of each read so that several small samples can be sequenced in one lane.

Is there a program that can be used to separate the reads with my barcode from the others?

Thanks.
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Old 01-04-2011, 06:59 AM   #2
hklein
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Hi agc,

the fastx_toolkit (http://hannonlab.cshl.edu/fastx_toolkit/) contains a barcode splitter.

Cheers,
Holger
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Old 01-05-2011, 05:34 AM   #3
agc
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Ended up writing a short python script that does this, although I also found FASTX:
http://hannonlab.cshl.edu/fastx_toolkit/download.html
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