SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Structural variations using Newbler mapper Soni Bioinformatics 2 12-06-2011 09:58 PM
finding structural variations without paired reads mike.t Bioinformatics 3 05-05-2011 10:23 AM
inGAP-sv: a new tool to identify and visualize structural variations biofqzhao Bioinformatics 0 02-20-2011 08:22 PM
Structural Variations sparks Bioinformatics 0 10-30-2008 02:16 PM

Reply
 
Thread Tools
Old 12-21-2013, 06:26 AM   #1
luciano.cascione
Junior Member
 
Location: Ohio (US)

Join Date: Jan 2013
Posts: 2
Default Structural Variations using RNA-Seq

Hello everybody,

I'm quite new in NGS. I'm looking for tools/stuff/idea to find Structural Variation (large deletion or tandem duplication) using RNA-Seq dataset (Illumina 100bp pair-end reads).

Could I use delly? This algorithm should work with DNA-Seq, may I use it with my RNA-Seq dataset?

So I look to the community if anyone can help me in my search for deletion.

Thank you for any help you can provide.

Luciano
luciano.cascione is offline   Reply With Quote
Old 01-08-2014, 12:06 AM   #2
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

I think finding structural variation in RNA-seq is tricky, because very hard to differentiate isoforms and real structural variations. So I prefer paired-end DNA-Seq to find large deletions.
TiborNagy is offline   Reply With Quote
Old 01-08-2014, 12:34 PM   #3
shi
Wei Shi
 
Location: Australia

Join Date: Feb 2010
Posts: 235
Default

Quote:
Originally Posted by luciano.cascione View Post
Hello everybody,

I'm quite new in NGS. I'm looking for tools/stuff/idea to find Structural Variation (large deletion or tandem duplication) using RNA-Seq dataset (Illumina 100bp pair-end reads).

Could I use delly? This algorithm should work with DNA-Seq, may I use it with my RNA-Seq dataset?

So I look to the community if anyone can help me in my search for deletion.

Thank you for any help you can provide.

Luciano
You may try the subjunc aligner in Subread package. It can find up to 200bp indels in RNA-seq data.
shi 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 06:12 AM.


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