Hello,

Yes, this tool functions on MAF input. For examples through several cases with this tool group, including this tool, please see:

" Making whole genome alignments usable for biologists" publication & supplemental.
https://main.g2.bx.psu.edu/u/dan/p/maf

"Using Galaxy" publication & supplemental. Protocol #5
https://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012

The public Main server is experiencing some performance issues right now, so please give it some time before trying out the exercises & your analysis. Reviewing the pages should be fine. Screencasts can be watched on any browser except Firefox (use Chrome, Safari)

Thanks,
Jen
Galaxy team

On 9/24/13 5:59 AM, Jennifer Di Tommaso wrote:
Hi,
I don't undestand how to use the tool "Stitch MAF blocks". I update a small bed file and now I need to run this tool, I don't understand the next step. I'm searching for Novel Linc in some RNA-seq data and I found the lncRscan tool (http://code.google.com/p/lncrscan/wiki/example) and now I have to use "Stitch MAF blocks".

The point is: I update the bed file, I select Fetch Alignments -> Stitch MAF blocks, and then I can do nothing, I can only choose among "locally cached alignments" and "alignments in your history". But MAF type/MAF file remain empty, in any case.

Can someone be so gentle to solve my problem? Do I need to download a MAF file? Is it normally on Galaxy server, but now it is down? How can I produce a MAF file selecting only some species (29 mammals)?

Thank you really much.

Jennifer


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