Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Convert paired-end, longer reads to single-end, shorter reads mlodato Bioinformatics 7 01-30-2016 06:47 AM
Samtools MPILEUP on single-end/paired-end data balthasar Bioinformatics 0 12-30-2014 05:55 AM
Treating paired end data as single end tirohia RNA Sequencing 11 03-17-2014 06:55 AM
Forcing paired-end data mapped as single-end in SAM puggie Bioinformatics 1 03-16-2013 11:50 AM
Does Cufflinks support single-end and paired end data together ? ersenkavak Bioinformatics 1 10-22-2010 08:26 AM

Thread Tools
Old 05-29-2015, 07:07 AM   #1
Junior Member
Location: Taipei

Join Date: May 2015
Posts: 1
Default Convert single-end data to paired-end

Hi, everybody,

I got single-end read data of RNAseq. Is there any software program that could convert single-end data into paired-end data so that I could use Chimerascan or other fusion-searching programs which only accept paired-end data?

Thanks a lot.

ccpan is offline   Reply With Quote
Old 05-29-2015, 07:33 AM   #2
Senior Member
Location: UK

Join Date: Jan 2010
Posts: 390

No, because the whole point of having paired end data for something like fusion detection relies on you having sequenced both ends of the same molecule.

You'd need to use a split-read approach.
Bukowski is offline   Reply With Quote
Old 05-29-2015, 10:08 AM   #3
Brian Bushnell
Super Moderator
Location: Walnut Creek, CA

Join Date: Jan 2014
Posts: 2,707

Actually, I have a tool for this purpose, bundled with BBMap. Usage: in=singles.fq out1=r1.fq out2=r2.fq overlap=0

This will generate paired reads from single-ended reads by cutting them in half. I have used it effectively for finding chimeras by mapping.
Brian Bushnell is offline   Reply With Quote

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 10:49 PM.

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