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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