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.cock@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.
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