Hi Felix It might be a little bit unusual to use the "generic feature format" (GFF) to show where your reads map....but strictly speaking mapped reads on a genome are 'features' as well. You can do it the following way: first use the "Convert SAM to interval" tool (NGS: SAM Tools), and use the "BED-to-GFF converter" (Convert Formats) I hope this helps, Hans On 02/18/2011 01:22 PM, Peter wrote:

On Fri, Feb 18, 2011 at 12:08 PM, Felix Hammer<hammerf@cip.ifi.lmu.de> wrote:

...

Hi, is there an easy way to use Galaxy to convert SAM to GFF? thx, Felix

How so?

SAM/BAM shows you where your reads map, GFF is used for annotation (e.g. where the genes are and what they may do).

Are you talking about using SAM/BAM transcriptome mapping (RNA-Seq) for gene finding?

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