Hi Amit, Without taking a look at your history, I'll have to make a guess. When you retrieve regions from UCSC, on the second step, right before you click "Send query to Galaxy", make sure that you have "Whole Gene" selected under "One record per", and that you are looking at a gene track and that the format was set to "BED" on the first page. Also be sure to Not include a track header. Thanks for using Galaxy, Dan On Oct 19, 2011, at 11:10 PM, Amit Indap wrote:

Hi Galaxy,

I am trying to stitch together MAF alignments for the coding sequence for a few genes of interest in Drosophila. I used UCSC to send the bed intervals of the coding exons of my gene and sent the output to Galaxy. But when I try and use the tool "Stitch Gene blocks" it complains that my bed is a bed3 and not a bed12.

I'm a bit rusty with my browser skills, but how can I send my output to Galaxy as a bed12 format so I can stitch my MAF blocks together?

Thanks for your help!

Amit

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