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Old 12-20-2013, 06:03 AM   #1
Location: Sherbrooke

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Default Unknown bases


I'm new to deep sequencing analysis and I was wondering if there is a tool on Galaxy that can remove reads containing unknown bases (N).

Thanks for your time
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Old 12-20-2013, 07:03 AM   #2
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Big up to Nick Loman for his script
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Old 12-20-2013, 07:16 AM   #3
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Since you want to do this in galaxy see slide #14 in this presentation:

Please keep in mind that if you use this tool on paired-end data in galaxy there is a chance of getting your R1-R2 files out-of-sync as far as the order of the reads is concerned.

Last edited by GenoMax; 12-20-2013 at 07:30 AM.
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