SEQanswers

Go Back   SEQanswers > Applications Forums > De novo discovery



Similar Threads
Thread Thread Starter Forum Replies Last Post
How to only select longest isoforms? henrik_licht Bioinformatics 1 10-16-2014 02:42 AM
cummeRbund get isoforms paolo.kunder Bioinformatics 6 04-23-2014 07:59 AM
BLAST for spliced isoforms? tboothby Bioinformatics 8 09-07-2011 08:20 AM
MIRA transcriptome assembly and isoforms JueFish Bioinformatics 5 02-02-2011 08:34 PM
Cufflinks-Tophat-isoforms ? repinementer Bioinformatics 1 07-19-2010 07:37 AM

Reply
 
Thread Tools
Old 06-22-2011, 02:12 AM   #1
papori
Senior Member
 
Location: berd

Join Date: Dec 2010
Posts: 181
Default looking for isoforms

Hey all,
i did de novo assembly for transcriptome . Now i want to look for isoforms .
do anyone familiar with software that doing it?

what are the automatics analysis tools for de novo assembly?
where to look for?

thanks!
papori is offline   Reply With Quote
Old 06-22-2011, 03:18 AM   #2
tir_al
Member
 
Location: Croatia

Join Date: Sep 2010
Posts: 22
Default

You could try the "Trinity pipeline". It does transcriptome reconstruction without the reference genome.

http://www.nature.com/nbt/journal/va.../nbt.1883.html

Best regards.
tir_al is offline   Reply With Quote
Old 06-22-2011, 03:23 AM   #3
papori
Senior Member
 
Location: berd

Join Date: Dec 2010
Posts: 181
Default

i used Trinity for the assembly...
papori 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 09:36 AM.


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