Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
cufflinks: reports non existing transcripts kenietz Bioinformatics 1 11-06-2012 09:49 AM
Integrating MiSeq in an existing HiSeq infrastructure GenoMax Illumina/Solexa 4 03-02-2012 03:16 PM
PubMed: Haplotype phasing: existing methods and new developments. Newsbot! Literature Watch 0 11-06-2011 02:30 AM
CLC bio partners with Ion Torrent to expand high-throughput sequencing support CLC bio Vendor Forum 0 04-16-2010 01:27 PM

Thread Tools
Old 05-26-2014, 12:40 AM   #1
Junior Member
Location: Bad Nauheim

Join Date: May 2014
Posts: 1
Default Expand existing transcriptome

I am new to working with NGS data. I want to add the information of new Sequence Reads to an existing transcriptome to possibly identify new transcripts. Does anyone have an idea of how to approach the matter? My first idea is mapping the reads to the trancriptome.
MaryBioInf is offline   Reply With Quote
Old 05-26-2014, 04:59 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,814

That would be one way to identify reads that are mapping to known transcripts.

You can also try to de novo assemble the entire set (or the reads left over after mapping above) using Trinity or Spades (if this is a prokaryotic/small genome).
GenoMax is offline   Reply With Quote
Old 05-26-2014, 12:57 PM   #3
Location: Berkeley

Join Date: Oct 2008
Posts: 16

Use Tophat and Cufflinks (Trapnell et al. Nature Protocols (2012); with the annotation as a guide.

I would not trust it for differential expression of isoforms, but for assembling new transcripts it works fairly well. Only use high quality reads for the assembly and be careful to filter after the final merge.
Darwin 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 12:46 PM.

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