Hi Peter, There isn't a built-in Galaxy tool to compute GC%, yet. You could perhaps use UCSC's hgGcPercent binary, which lets you compute GC% for BED intervals. You can find the same here: http://genome.ucsc.edu/FAQ/FAQdownloads#download27
Thanks, Guru. On Thu, Apr 14, 2011 at 9:11 AM, Peter Cock <p.j.a.c...@googlemail.com>wrote: > Hi all, > > Are there any built in Galaxy tools that I have missed to do with GC > percentage (or indeed, AT percentage)? > > I'm thinking of a tool to calculate the GC percentage (and perhaps > related statistics like counts/percentages of A, C, G, T), and perhaps > a related tool to filter on GC. Possible use cases include filtering > NGS reads to remove high/low GC reads from a contaminate. > > Slightly more complicated, right now I want to calculate the GC (or in > fact AT) percentage from the first and last ~20 (configurable) bases. > In this case I am looking for (and filtering on) AT rich ends of > contigs which may be indicative of viral sequences. A very similar > task would be looking for (and filtering on) poly A tails of mRNA, or > if sequenced from the reverse strand, a poly T start. > > Peter > ___________________________________________________________ > The Galaxy User list should be used for the discussion of > Galaxy analysis and other features on the public server > at usegalaxy.org. Please keep all replies on the list by > using "reply all" in your mail client. For discussion of > local Galaxy instances and the Galaxy source code, please > use the Galaxy Development list: > > http://lists.bx.psu.edu/listinfo/galaxy-dev > > To manage your subscriptions to this and other Galaxy lists, > please use the interface at: > > http://lists.bx.psu.edu/ > -- Graduate student, Bioinformatics and Genomics Makova lab/Galaxy team 505 Wartik lab University Park PA 16802 g...@psu.edu
___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list: http://lists.bx.psu.edu/listinfo/galaxy-dev To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
