Unknown bases

[FrankiB]

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

[TonyBrooks]

https://github.com/nickloman/xbase/blob/master/short-read-assembly/eliminate_n_paired.py

Big up to Nick Loman for his script

[GenoMax]

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.