[galaxy-user] Trimming small RNA

2011-09-11 Thread Thiago Mafra
Hello everybody, I have sequences of small RNA's from 18 to 35nt and accurate trim the sequences of the adapters before aligning the reads with the reference genome. Are there any tools available to it in the Galaxy? Thanks. -- Thiago Mafra Batista Biólogo Molecular Doutorando em Bioinformática

Re: [galaxy-user] Trimming small RNA

2011-09-11 Thread Richard Mark White
Hi,   This must seem like a newbie question but I cant get a clear answer.  My understanding from the galaxy wiki page http://wiki.g2.bx.psu.edu/Learn/FAQ#Learn.2BAC8-FAQ.Interval_and_BED_format is that all intervals in galaxy are 0 based, start inclusive end exclusive.   but when i use

Re: [galaxy-user] Trimming small RNA

2011-09-11 Thread James Robinson
Hi Rich, That is consistent with the BED format, that is in BEDs 0 based coordinate system the SNP is at 1056309. In the more common 1 based system this translates to 1056310. If the end were inclusive the SNP would be at 1056309-1056310 in BED world, that is it would take 2 positions. The