Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Antisense RNA analysis from strand specific RNA-seq Pengfei Liu Bioinformatics 0 02-19-2014 05:17 AM
RNA-seq and sense/antisense expression differences JueFish Bioinformatics 7 12-12-2013 02:44 PM
Quantifying antisense transcription from non-strand Specific RNA seq aslihan Bioinformatics 1 05-06-2013 07:39 AM

Thread Tools
Old 12-02-2014, 02:08 AM   #1
Location: Internet

Join Date: Aug 2014
Posts: 15
Default RNA-seq - Recovering antisense RNA counts

Hello to all,

I have RNA-seq data generated with the mRNA stranded protocol of Illumina (which is a dUTP protocol).

Generally, I used TopHat/Bowtie and htseq-count to align and quantify my data. So, I have done that, with the "fr-firststrand" for TopHat and "stranded=reverse" for HTSeq.

Now, I want to separate the sense and antisense RNAs from my data. I have seen two possibilities :

With Htseq-count => We can use the --stranded=yes option, to keep all the anti-sense expression counts and the --stranded=reverse option, to keep all the sense counts.
samtools view -F 16 Reads.bam => to obtain reads that map on forward strand
samtools view -f 16 Reads.bam => to obtain reads that map on forward strand
I think there is a biological principle that I do not quite understand.

For the second option, which uses samtools, it is assumed that all reads that align to the reverse strand correspond to antisense transcripts ? and all reads that align to the forward strand correspond to sense transcripts ?

In fact, simply, I do not understand the antisense selection method.

Can anyone explain this to me? And what is the best method for you? The two methods are equivalent?

Thanks in advance to all of you.

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 11:22 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2022, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO