Trans-abyss reference genome??

[ritzriya]

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..

[ritzriya]

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

Please help..

[jts]

You should try posting your questions to the abyss mailing list:

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

[ritzriya]

Okay, have done that.. now will wait for the answer..

[jgoecks]

There is also a group devoted to trans-abyss:

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

Best,
J.