Latest
Open
RNA-Seq
ChIP-Seq
SNP
Assembly
Forum
Planet
All »
Home
Log In
Question: Problem With Gmaj
0
gravatar for Ross Hardison
12.3 years ago by
Ross Hardison • 270
United States
Ross Hardison • 270 wrote:
I'm trying to use the GMAJ tool on Galaxy, but get this error: Error loading alignments from bundled file "input.maf": edu.psu.bx.gmaj.BadInputExceptions: Sequence length contradiction" s baboon.1 26891 63 + 1248010 TCAG... Current = 1248010. Previous = 550206 The maf files were extracted using the "Extract MAF blocks" tool, for TBA ENCODE alignments. The maf data are at http://main.g2.bx.psu.edu/display?id=3054
galaxy • 977 views
ADD COMMENT • link •
modified 12.3 years ago by James Taylor • 320 • written 12.3 years ago by Ross Hardison • 270
0
gravatar for James Taylor
12.3 years ago by
James Taylor • 320
United States
James Taylor • 320 wrote:
Ross, The problem here is that there are multiple sequences with the name 'baboon.1'. In fact, in the ENCODE TBA alignments there is a different 'baboon.1' for every ENCODE region, so when you concatenate MAFs across multiple regions you get a result that GMAJ (rightly) cannot understand. To correct this I think the only thing we can do is change the MAFs provided by the encode group so that every orthologous sequence has a unique name across encode regions. So baboon.1 -> baboon.ENm001_1, and so on. All, would such a change break any existing tools / analysis? -- jt
ADD COMMENT • link written 12.3 years ago by James Taylor • 320
No conflicts on my end. Actually, it would be a rather convenient (and accurate) annotation to refer to the aligned species by region. -David
ADD REPLY • link written 12.3 years ago by D C King • 10
This sounds like the correct solution, and I cannot think of any tools which would be broken by doing this. Dan
ADD REPLY • link written 12.3 years ago by Dan Blankenberg • 130
Please log in to add an answer.

Similar posts • Search »

Content
Help
Access
Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 173 users visited in the last hour