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Old 12-20-2013, 05:03 AM   #1
FrankiB
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Location: Sherbrooke

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Default Unknown bases

Hi,

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, 06:03 AM   #2
TonyBrooks
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https://github.com/nickloman/xbase/b...te_n_paired.py

Big up to Nick Loman for his script
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Old 12-20-2013, 06:16 AM   #3
GenoMax
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Since you want to do this in galaxy see slide #14 in this presentation: http://www.bx.psu.edu/~dan/presentat...h_2011_ngs.pdf

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 06:30 AM.
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