Question: Denovo with tophat
0
gravatar for pkeneilwe
4.0 years ago by
pkeneilwe0
South Africa
pkeneilwe0 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
ADD COMMENTlink modified 4.0 years ago by Philipe Moncuquet40 • written 4.0 years ago by pkeneilwe0

Yes, TopHat and cufflinks should help you.

ADD REPLYlink written 4.0 years ago by Bjoern Gruening5.1k
Thanks. ..so how do I create a de novo reference? Can I use clc bio to create it, then proceed with tophat?
ADD REPLYlink written 4.0 years ago by pkeneilwe0
Thanks. ..so how do I create a de novo reference? Can I use clc bio to create it, then proceed with tophat?
ADD REPLYlink written 4.0 years ago by pkeneilwe0
Thanks. ..so how do I create a de novo reference? Can I use clc bio to create it, then proceed with tophat?
ADD REPLYlink written 4.0 years ago by pkeneilwe0

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

ADD REPLYlink written 3.9 years ago by Bjoern Gruening5.1k
0
gravatar for Philipe Moncuquet
4.0 years ago by
Australia
Philipe Moncuquet40 wrote:

You might want to read this http://bioinformatics.oxfordjournals.org/content/25/9/1105.long

ADD COMMENTlink written 4.0 years ago by Philipe Moncuquet40
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