SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Mapping paired-end stranded RNA-seq data hubin.keio Bioinformatics 3 03-28-2013 02:10 PM
Tophat reads that weren't used for mapping? vkartha Bioinformatics 0 04-18-2012 07:45 AM
Does tophat allow indel mapping in reads? louis7781x Bioinformatics 3 07-21-2011 04:26 AM
What does TopHat do with discordantly mapping PE reads? krobison Bioinformatics 0 10-10-2010 05:28 PM
Tophat...Mapping reads against Reference with Bowtie [FAILED] Brajbio Bioinformatics 0 06-02-2010 12:33 AM

Reply
 
Thread Tools
Old 02-14-2014, 04:27 AM   #1
JonB
Member
 
Location: Norway

Join Date: Jan 2010
Posts: 83
Default Mapping stranded smallRNA reads with TopHat

Hi,

I have short reads (max 50 nts, mostly 20-40 nts) that are from a stranded ligated Illumina library. I could't find if Bowtie2 has a stranded option so I use the TopHat fr-secondstrand option. But I don't expect my reads to be spliced so is there an option to skip the read segmentation? Or should I use other mappers for this job?

Thanks,

Jon
JonB is offline   Reply With Quote
Old 02-14-2014, 05:05 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,049
Default

You can try the subread aligner and featureCounts downstream.
GenoMax is offline   Reply With Quote
Reply

Tags
bowtie 2, mapping, small rna, tophat 2

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 02:12 PM.


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