SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
Counting alignments mparida85 Introductions 6 06-08-2014 10:33 AM
miRNA aligning/counting kmcarr Bioinformatics 28 02-08-2013 02:35 PM
Htseq counting maize RNA Sequencing 2 12-05-2012 11:50 PM
Counting of regions within a segment DrD2009 Bioinformatics 0 01-08-2012 11:53 AM
Isotigs counting nicedad General 0 10-31-2011 05:44 AM

Reply
 
Thread Tools
Old 12-03-2015, 02:21 PM   #1
bfp7
Junior Member
 
Location: NH

Join Date: Nov 2015
Posts: 9
Default counting with kallisto

I want to count RNA-seq reads but I do not have a reference transcriptome. Can I align the reads to a trinity assembly? If so, how do I do this?
bfp7 is offline   Reply With Quote
Old 12-03-2015, 02:40 PM   #2
dpryan
Devon Ryan
 
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,479
Default

Sure, just treat the trinity assembly as the reference transcriptome (I assume you assembled the transcriptome rather than the genome).
dpryan is offline   Reply With Quote
Old 12-03-2015, 02:51 PM   #3
bfp7
Junior Member
 
Location: NH

Join Date: Nov 2015
Posts: 9
Default

OK, thanks. I'll give it a go.
bfp7 is offline   Reply With Quote
Reply

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 11:34 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO