SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Tophat --library-type option Wei-HD Bioinformatics 5 05-27-2013 07:15 AM
Top Hat and Illumina standard protocol Fiki RNA Sequencing 0 06-26-2012 05:43 AM
comparing Bowtie/DESeq and Top-Hat/Cufflinks results maryb Bioinformatics 5 03-13-2012 08:46 AM
Questions about Top-Hat and Paired End Reads Cirno Bioinformatics 4 12-03-2011 12:07 PM
cufflinks library-type option damiankao Bioinformatics 0 11-26-2010 04:08 AM

Reply
 
Thread Tools
Old 06-26-2012, 06:10 AM   #1
Fiki
Junior Member
 
Location: Spain

Join Date: Jun 2012
Posts: 3
Question Top Hat and library option

I've got a RNA-Seq experiment, whose author said in the paper that used Strand-specific RNA-Seq. Reading the experimental procedures, I've found ,briefly,that they generated first strand and during the second strand synthesis they add dUTP (here the paper).

The problem is when I've to do alignments using TopHat. TopHat documentation says that we've to use fr-firststrand with dUTP, however it says too that we've to use fr-secondstrand when the strand generated during second strand synthesis is sequenced.

any ideas?

Thanks!
Fiki is offline   Reply With Quote
Reply

Tags
library, strand specific, tophat

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 05:38 PM.


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