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Question: Denovo with tophat
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gravatar for pkeneilwe
4.0 years ago by
pkeneilwe • 0
South Africa
pkeneilwe • 0 wrote:
Hello everyone. I am new to RNA Seq and need help. I just want to ask if it is right to do de novo RNA Seq analysis using a reference that I created(from assembly) with tophat? Thanking you in advance. Keneilwe
de novo • 1.4k views
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modified 4.0 years ago by Philipe Moncuquet • 40 • written 4.0 years ago by pkeneilwe • 0

Yes, TopHat and cufflinks should help you.

ADD REPLY • link written 4.0 years ago by Bjoern Gruening ♦ 5.1k
Thanks. ..so how do I create a de novo reference? Can I use clc bio to create it, then proceed with tophat?
ADD REPLY • link written 4.0 years ago by pkeneilwe • 0
Thanks. ..so how do I create a de novo reference? Can I use clc bio to create it, then proceed with tophat?
ADD REPLY • link written 4.0 years ago by pkeneilwe • 0
Thanks. ..so how do I create a de novo reference? Can I use clc bio to create it, then proceed with tophat?
ADD REPLY • link written 4.0 years ago by pkeneilwe • 0

Yes you can try this or you can try to assemble your RNA-Seq reads with Trinity.

ADD REPLY • link written 3.9 years ago by Bjoern Gruening ♦ 5.1k
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gravatar for Philipe Moncuquet
4.0 years ago by
Philipe Moncuquet • 40
Australia
Philipe Moncuquet • 40 wrote:

You might want to read this http://bioinformatics.oxfordjournals.org/content/25/9/1105.long
ADD COMMENT • link written 4.0 years ago by Philipe Moncuquet • 40
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