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Old 12-21-2010, 01:02 AM   #1
ritzriya
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Arrow Trans-abyss reference genome??

Dear All,

After a lot of trouble with getting my Input file correct for Trans-abyss, I am unable to understand why does it require a Reference genome to run? It uses mm9 (mouse) or hg18 (human) only as reference.

Why in the first place will I go for trans-abyss if I had a reference genome? It is an RNA-seq data, on which I have already executed ABySS- it produced contigs.fa.

Why is this contigs.fa not being used as an input file directly to generate transcripts?

Any insights on these two queries will help me a lot to understand the tool better!!

Thanks in advance..
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Old 01-06-2011, 10:24 PM   #2
ritzriya
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Arrow

No answers yet!! 88 viewers but no solution to this problem?

Please help..
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Old 01-07-2011, 12:29 AM   #3
jts
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You should try posting your questions to the abyss mailing list:

http://groups.google.com/group/abyss-users
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Old 01-07-2011, 01:44 AM   #4
ritzriya
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Okay, have done that.. now will wait for the answer..
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Old 01-13-2011, 06:32 AM   #5
jgoecks
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There is also a group devoted to trans-abyss:

http://groups.google.com/group/trans-abyss

Best,
J.
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