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.
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 &
"Using Galaxy" publication & supplemental. Protocol #5
The public Main server is experiencing some performance issues right
now, so please give it some time before trying out the exercises &
analysis. Reviewing the pages should be fine. Screencasts can be
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