SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq: TopHat-Fusion: an algorithm for discovery of novel fusion transcripts. Newsbot! Literature Watch 5 07-13-2013 12:02 AM
Gene Fusion and chimeric transcripts harshinamdar Bioinformatics 3 11-03-2012 03:02 AM
detect fusion gene from Solid single end 50bp reads( colorspace) yinxiaohe SOLiD 5 12-16-2011 04:39 AM
Fusion gene detect tools for Solid (colorspace)single end 50bp RNA-seq data yinxiaohe RNA Sequencing 3 08-22-2011 06:04 PM
Detection of Fusion Gene Events from RNASeq PE reads zee Bioinformatics 2 05-12-2011 09:14 PM

Reply
 
Thread Tools
Old 02-28-2011, 01:18 AM   #1
kenosaki
Member
 
Location: Tokyo, Japan

Join Date: May 2010
Posts: 27
Default Gene fusion detection

Hi,
I am wondering if detection of fusion gene is possible using a GA's single but relatively long (70-100 bp) read RNA-Seq data.
I know some software can detect fusion gene from paired-end dataset, but not sure how it's possible in a single read.
Any suggested tools or method?

Thanks,
Ken
kenosaki is offline   Reply With Quote
Old 02-28-2011, 07:47 AM   #2
krobison
Senior Member
 
Location: Boston area

Join Date: Nov 2007
Posts: 747
Default

It is certainly doable but your sensitivity will be inferior to paired end data.

Bowtie can be "tricked" into just aligning one end or the other of your reads (using the 3' & 5' trimming options); these alignments could be post-processed to look for split reads.

Alternatively, you could split the reads & create two files as though you had paired-end data.
krobison is offline   Reply With Quote
Old 02-28-2011, 04:17 PM   #3
kenosaki
Member
 
Location: Tokyo, Japan

Join Date: May 2010
Posts: 27
Default

Quote:
Originally Posted by krobison View Post
Alternatively, you could split the reads & create two files as though you had paired-end data.
That's what I thought at first, but I'm not sure where I should split the read out. As you know, the first half has higher quality than the last half has.

But thanks, bowtie could be my option.
kenosaki is offline   Reply With Quote
Old 03-01-2011, 10:51 AM   #4
HESmith
Senior Member
 
Location: Bethesda MD

Join Date: Oct 2009
Posts: 506
Default

Hi Ken,

We used split-end alignment to map insertion elements, but the same approach can be used to identify any novel junctions (such as gene fusions). The most important consideration is the size of the gap between the ends, since that's where the novel junction maps. For 70bp reads, mapping 25bp from each end leaves a 20bp window where the junction can fall. A detailed description of this method was described in the February 2011 issue of Biotechniques.

-Harold
HESmith is offline   Reply With Quote
Old 03-01-2011, 12:38 PM   #5
JohnK
Senior Member
 
Location: Los Angeles, China.

Join Date: Feb 2010
Posts: 106
Default

Quote:
Originally Posted by HESmith View Post
Hi Ken,

We used split-end alignment to map insertion elements, but the same approach can be used to identify any novel junctions (such as gene fusions). The most important consideration is the size of the gap between the ends, since that's where the novel junction maps. For 70bp reads, mapping 25bp from each end leaves a 20bp window where the junction can fall. A detailed description of this method was described in the February 2011 issue of Biotechniques.

-Harold
can you cite this? i tried to find it but had no luck.
JohnK is offline   Reply With Quote
Old 03-01-2011, 12:42 PM   #6
HESmith
Senior Member
 
Location: Bethesda MD

Join Date: Oct 2009
Posts: 506
Default

The link is here. In the supplemental materials, we describe the identification of two large deletions by split-end reads that were further apart than the read length. A similar strategy would identify fusion genes.

Harold
HESmith is offline   Reply With Quote
Old 03-02-2011, 05:57 AM   #7
JohnK
Senior Member
 
Location: Los Angeles, China.

Join Date: Feb 2010
Posts: 106
Default

Quote:
Originally Posted by HESmith View Post
The link is here. In the supplemental materials, we describe the identification of two large deletions by split-end reads that were further apart than the read length. A similar strategy would identify fusion genes.

Harold
Thank you, Harold!
JohnK is offline   Reply With Quote
Old 03-02-2011, 11:15 PM   #8
kenosaki
Member
 
Location: Tokyo, Japan

Join Date: May 2010
Posts: 27
Default

Thanks guys, I'll try them.
kenosaki 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 06:27 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO