SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Best pipeline for DE and fusion gene using tophat? ymc Bioinformatics 14 08-17-2013 06:21 PM
How to filter fusion gene hypno RNA Sequencing 0 07-26-2013 08:47 AM
Gene Fusion Annotation pipeline fabate RNA Sequencing 6 04-04-2013 05:47 AM
Gene Fusion and chimeric transcripts harshinamdar Bioinformatics 3 11-03-2012 03:02 AM
Gene fusion detection kenosaki Bioinformatics 7 03-02-2011 11:15 PM

Reply
 
Thread Tools
Old 08-23-2013, 02:03 PM   #1
statsteam
Member
 
Location: Californica

Join Date: Sep 2009
Posts: 19
Default gene fusion question

Dear all,

I am new to the gene fusion field and I would like to ask a basic question.

What is a good and easy program to use to detect gene fusion form RNA-Seq data?

Thank you in advance,
-Statsteam
statsteam is offline   Reply With Quote
Old 08-25-2013, 06:20 PM   #2
matrix731
Junior Member
 
Location: Shenzhen

Join Date: Oct 2011
Posts: 4
Default

Maybe you can try SOAPfuse:
Quote:
Jia W, Qiu K, He M, et al. SOAPfuse: an algorithm for identifying fusion transcripts from paired-end RNA-Seq data[J]. Genome biology, 2013, 14(2): R12.
and download from here http://soap.genomics.org.cn/soapfuse.html
matrix731 is offline   Reply With Quote
Old 08-26-2013, 09:40 AM   #3
statsteam
Member
 
Location: Californica

Join Date: Sep 2009
Posts: 19
Default

Thanks a lot! By the way, it seems that SOAPfuse requires paired-end reads while the reads I have is single-end. Any other tools for this purpose?
statsteam is offline   Reply With Quote
Reply

Tags
fusion, gene fusion, rna-seq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 05:53 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO