SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Gene Fusion and chimeric transcripts harshinamdar Bioinformatics 3 11-03-2012 04:02 AM
detect fusion gene from Solid single end 50bp reads( colorspace) yinxiaohe SOLiD 5 12-16-2011 05:39 AM
RNA-Seq: Detection of splicing events and multiread locations from RNA-seq data based Newsbot! Literature Watch 0 10-26-2011 03:50 AM
Gene fusion detection kenosaki Bioinformatics 7 03-03-2011 12:15 AM
Detection of alternative splicing events from 454 output Khanjan 454 Pyrosequencing 15 11-15-2010 08:56 PM

Reply
 
Thread Tools
Old 10-24-2010, 01:27 AM   #1
zee
NGS specialist
 
Location: Malaysia

Join Date: Apr 2008
Posts: 249
Default Detection of Fusion Gene Events from RNASeq PE reads

Hi Everybody,

I am looking for the best strategy for finding gene fusion events in some human resequencing RNASeq paired-end reads.
At present there is one package I am aware of called DeFuse, however I think that tools such as BreakDancer, Breakway and Hydra-SV would be suitable for this task with some downstream operations.

I have my reads mapped to HG18 with novoalign in BAM format. Some pointers from people with experience would be great.

Thanks
zee is offline   Reply With Quote
Old 10-24-2010, 07:48 PM   #2
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
Default

You might also check out Trans-ABySS and FusionSeq

I haven't (yet) gotten experience with any of these.
krobison is offline   Reply With Quote
Old 05-12-2011, 10:14 PM   #3
kissthefuture
Junior Member
 
Location: china

Join Date: Apr 2011
Posts: 6
Default

I think you can look this page :http://compbio.bccrc.ca/?page_id=600

there is a workflow for you
kissthefuture is offline   Reply With Quote
Reply

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 01:29 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO