Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Multiple sequence alignment analysis biobudhan Bioinformatics 1 03-28-2012 08:11 PM
Samtools (sequence alignment/mapping) wisosonic Bioinformatics 2 03-28-2011 05:31 AM
sequence alignment report slny Bioinformatics 3 03-17-2011 08:45 AM
Short sequence alignment rboettcher Bioinformatics 9 03-17-2011 03:35 AM
Sequence Alignment Quality Control nilshomer Bioinformatics 4 02-06-2010 08:24 AM

Thread Tools
Old 01-18-2011, 10:01 AM   #1
Location: USA

Join Date: Nov 2010
Posts: 56
Default Sequence direction in alignment

I have a simple question. We use illumina reads for a RNA seq analysis. when i visualize the alignment using IGV, i see reads that are pointed in two orientations? I would expect the reads to be in the 5'->3' but find both 5 to 3 and 3 to 5 orientation. Why do i find the mix of sequences? Does such a mix limit the analysis?

newbietonextgen is offline   Reply With Quote
Old 01-18-2011, 12:41 PM   #2
Senior Member
Location: San Diego

Join Date: May 2008
Posts: 912

There are strand-specific Illumina preps, but if the RNA is turned in to cDNA, strand info will be lost.

You can talk to whomever preps the RNA, but you data sounds like it came from a non-strand-conserving prep.

Last edited by swbarnes2; 01-18-2011 at 03:35 PM. Reason: typos
swbarnes2 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 08:14 PM.

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