Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Help with RNA-seq and strand specific mapping weirdkid Bioinformatics 16 11-24-2015 03:35 AM
mapping strand-specific RNA-seq reads using TopHat caswater Bioinformatics 2 03-17-2015 08:27 AM
Mixing strand-specific and non strand-specific reads in RNA-seq alexanderxcy Bioinformatics 2 08-27-2013 01:39 AM
Mapping strand-specific data with TopHat Comosus RNA Sequencing 6 08-13-2012 01:25 AM
strand specific RNA-seq mapping qqtwee RNA Sequencing 1 07-10-2012 09:23 PM

Thread Tools
Old 01-08-2019, 03:22 AM   #1
Junior Member
Location: Germany

Join Date: Jan 2019
Posts: 1
Default Strand Specific mapping


I would like to do strand specific mapping to a set of bacterial RNA-Seq files. The libraries were prepared using the KAPA hyperprep kit and should "by definition" be strand specific. I used bbmap for mapping (a tool I often use) but the result, as viewd in Artemis suggests there is no strand specific data i.e. both strands are nearly mirror one of the other.

Before assuming the sequencing center did something wrong - I would like to be sure I am doing the mapping correctly.

can someone please advise on the parameters for BBMAP (or another tool if needed) to obtain strand specific mapping.

ionescu is offline   Reply With Quote

bbmap, mapping, rna-seq, strand-specific

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 04:27 PM.

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