SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
directional mRNA sequencing on amplified RNA papori RNA Sequencing 2 12-01-2011 02:06 AM
TruSeq small RNA for directional sequencing ambmor RNA Sequencing 3 09-15-2011 01:11 PM
Tophat library-type about the Directional Ligation sequencing (DeLi-seq) strategy evergreen Bioinformatics 0 09-08-2011 08:12 PM
RNA-Seq: Directional RNA deep sequencing sheds new light on the transcriptional respo Newsbot! Literature Watch 0 06-30-2011 03:00 AM
Directional RNA sequencing protocols bluefin Illumina/Solexa 3 06-12-2010 07:35 PM

Reply
 
Thread Tools
Old 01-03-2012, 02:29 AM   #1
frymor
Senior Member
 
Location: Germany

Join Date: May 2010
Posts: 149
Unhappy directional vs. non-directional sequencing

Hi,

Can someone please explain the difference between the directional and the non-directional sequencing methods?

I was looking for articles or sites which can explain it, especially the results one get from such run.

We have our results. This suppose to be a non-directional RNA-seq. The question was now, if we can extract the strand information from these data. I mean, is there a way to know if a strand belongs to the + or - strand?
In the bam file we have these results, but as far as I understand it, this information says only if the read was mapped to the forward or backward strand.

Am I wrong with this assumption?

I would appreciate ant information which will help me/us better understand the difference between the two technologies.

Thanks
A.
frymor is offline   Reply With Quote
Old 01-03-2012, 03:20 AM   #2
henry.wood
Member
 
Location: Leeds, UK

Join Date: Apr 2010
Posts: 63
Default

It's due to a difference in the library prep. Directional RNA-seq keeps the strand information by only making the cDNA in one direction, non-directional will make cDNA in both directions, so you have no way of knowing if your sequence read is in the same direction as the original transcription.
henry.wood is offline   Reply With Quote
Reply

Tags
directional rna-seq, directionality, non-directional rna-seq

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 07:03 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO