Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Clontech Stranded mRNA-Seq for Illumina: Two peaks in library? Innovelty Sample Prep / Library Generation 7 07-09-2014 10:43 AM
silly question r.e. TruSeq stranded mRNA sweetph3 Illumina/Solexa 2 03-21-2014 12:20 PM
Sequencing bacterial mRNA with Illumina stranded kits Noa RNA Sequencing 1 11-14-2012 03:13 AM
PubMed: Identification of differentially expressed sense and antisense transcript pai Newsbot! Literature Watch 0 07-21-2009 05:00 AM

Thread Tools
Old 09-24-2014, 05:57 AM   #1
Location: Internet

Join Date: Aug 2014
Posts: 15
Default Identifying antisense transcript with stranded mRNA-seq.

Hello to all,

I have one dataset that contains samples (2 conditions in 2 replicates) sequenced with "TruSeq Stranded mRNA Sample Prep Kit" : directional mRNA-seq.

How is it possible to study the antisense transcripts? In fact, I have theoretical and technical questions about it.

- antisense transcripts have as template the sense strand of DNA (and thus have the same sequence as the antisense strand of DNA) ? So antisense transcripts are transcribed from + strand ? and conversely, sense transcripts have as template the antisense strand of DNA (and thus have the same sequence as the sense strand of DNA) ?

- when I align my data with the TopHat tool (with fr-firstrand option, because this is a dUTP protocol), I have a XS:A tag by read, following by + or -. So, reads that are tagged by XS:A:+ correspond to sense transcripts and reads that are tagged by XS:A:- correspond to antisense transcripts ?

- in this topic "", Chung-Chau Hon said : "If a read is mapped on a feature specified in the GTF, the XS tag would always be on the same strand of the feature not matter what strand the read is mapped to. This would create wrong counts is there are unannotated antisense transcripts.". How do you study these antisense transcripts?

Thank you in advance for your response.
a.kmg 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 08:57 AM.

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