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Old 06-11-2015, 05:42 AM   #1
padmoo
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Location: Norwich

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Default PrinSeq paired reads and zipped

Hi everyone,

I'm looking for a solution to run PrinSeq on paired reads with .gz files.
I found this solution for single reads: http://sourceforge.net/p/prinseq/mai...sage/29201234/

and was wondering if there is a possibility to do something similar for paired reads.

Does anyone have an idea?

Thanks!

Padmoo
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Old 06-11-2015, 06:06 AM   #2
GenoMax
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You had some trouble with cutadapt earlier. Can I suggest that you try bbduk.sh from BBMap for trimming your data. It is straightforward to use and being a java program will run on PC/Mac/Unix.
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