Question: Maf Alignments
gravatar for Stewart Stevens
10.0 years ago by
Stewart Stevens20 wrote:
Hi, I have a local Galaxy instance. ( galaxy) A problem I'm having is when I try to extract a multiple alignment I get an error, "The MAF source specified (28_WAY_MULTIZ_hg18) appears to be invalid.," The background is that I have downloaded the alignment from and modified the maf_index.loc file according to the commented example. I'm new to python but I did have a look in the debugger and it seems to be missing an index file. The parameters it has loaded from maf_index.loc appear to be as expected. I'm guessing with more looking at the code it will become clear that a script to produce these indexes from mafs needs to be run. Or should these indexes be being built on the fly? Maybe someone can save me a load more digging? Thanks if you can! Cheers, Stewart -- Stewart Stevens Software Developer - Integrated Genomics University of Otago Department of Biochemistry Tel: +64(0)3 479 7863 Fax: +64(0)3 479 7866
galaxy • 913 views
ADD COMMENTlink modified 10.0 years ago by Daniel Blankenberg ♦♦ 1.7k • written 10.0 years ago by Stewart Stevens20
gravatar for Daniel Blankenberg
10.0 years ago by
Daniel Blankenberg ♦♦ 1.7k
United States
Daniel Blankenberg ♦♦ 1.7k wrote:
Hi Stewart, You are correct in that you need to create indexes for the MAF files. A script to create indexes is included in the bx-python package (named in the scripts directory of this package), which is distributed as an egg with Galaxy. Dan
ADD COMMENTlink written 10.0 years ago by Daniel Blankenberg ♦♦ 1.7k
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