RNA-SEQ with no genome

dror · 10-23-2010, 11:56 PM

Can i do RNA SEQUENCING without having the genome?

kopi-o · 10-24-2010, 12:42 AM

Yes, you can.

dror · 10-24-2010, 12:53 AM

Can you recommend me where to begin?

kopi-o · 10-24-2010, 12:58 AM

It's hard to be specific without knowing what you want to do, but generic advice wouild be to start by reading this review paper:

http://www.ncbi.nlm.nih.gov/sites/en...earch=19015660

Then go on to more specialized papers, or search this forum, for more information about "transcriptome assembly".

protist · 10-24-2010, 06:01 AM

Two recent papers discuss methodology and strategy:

De novo assembly and analysis of RNA-seq data - Nature Methods 2010
http://www.nature.com/nmeth/journal/...meth.1517.html

and a News & Views Article from Nature Biotechnology 2010
Advancing RNA-Seq analysis - New methods for analyzing RNA-Seq data enable de novo reconstruction of the transcriptome
http://www.nature.com/nbt/journal/v2...t0510-421.html

dror · 10-26-2010, 05:36 AM

thanks mates!

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10-23-2010, 11:56 PM	#1
dror Member Location: T"A Join Date: May 2010 Posts: 18	RNA-SEQ with no genome Can i do RNA SEQUENCING without having the genome?

10-24-2010, 06:01 AM	#5
protist Senior Member Location: Ireland Join Date: Jan 2009 Posts: 101	RNA-SEQ with no genome Two recent papers discuss methodology and strategy: De novo assembly and analysis of RNA-seq data - Nature Methods 2010 http://www.nature.com/nmeth/journal/...meth.1517.html and a News & Views Article from Nature Biotechnology 2010 Advancing RNA-Seq analysis - New methods for analyzing RNA-Seq data enable de novo reconstruction of the transcriptome http://www.nature.com/nbt/journal/v2...t0510-421.html

10-24-2010, 12:42 AM	#2
kopi-o Senior Member Location: Stockholm, Sweden Join Date: Feb 2008 Posts: 319	Yes, you can.

10-24-2010, 12:53 AM	#3
dror Member Location: T"A Join Date: May 2010 Posts: 18	Can you recommend me where to begin?

10-24-2010, 12:58 AM	#4
kopi-o Senior Member Location: Stockholm, Sweden Join Date: Feb 2008 Posts: 319	It's hard to be specific without knowing what you want to do, but generic advice wouild be to start by reading this review paper: http://www.ncbi.nlm.nih.gov/sites/en...earch=19015660 Then go on to more specialized papers, or search this forum, for more information about "transcriptome assembly".

10-26-2010, 05:36 AM	#6
dror Member Location: T"A Join Date: May 2010 Posts: 18	thanks mates!