Question

How to set the blast database of TopHat-Fusion

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6.8 years ago

shiyang93 ▴ 70

I am using tophat fusion. My RNA-Seq data are from human, do I need to download the other_genomic* and nt* database from blast database as suggested by the user manual of TOPHAT-Fusion? http://ccb.jhu.edu/software/tophat/fusion_tutorial.shtml Anyone who is familiar with tophat can tell me? Thanks!

blast tophat database gene fusion • 1.9k views

ADD COMMENT • link updated 6.8 years ago by Istvan Albert 100k • written 6.8 years ago by shiyang93 ▴ 70

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I have the same questions. Were you able to get TopHat-Fusion working with only the human_genomic* files?

ADD REPLY • link 6.2 years ago by kylevoyto ▴ 20

score 1 · Answer 1 · 2017-06-21

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6.8 years ago

Istvan Albert 100k

Since nt also contains the human genomic data it sounds like the other databases would only be needed when processing data other than human.

ADD COMMENT • link 6.8 years ago by Istvan Albert 100k

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Thank you very much! By the way, there are only human_genomic.00 -08, 10 - 16, 18 -21 on the blast database, no 09 and 17. I do not know if this human_genomic* database is intact. Could you give me some advice?

ADD REPLY • link 6.8 years ago by shiyang93 ▴ 70