SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Suspiciously low read numbers with shotgun pipeline compared to amplicon pipeline Krisztab 454 Pyrosequencing 0 03-27-2014 07:05 AM
What is the best and RAM efficient pipeline for de novo assembly of... Diegodescarpates Bioinformatics 4 02-05-2013 08:25 AM
Typical TopHat/Cufflinks pipeline? Aurelien Mazurie Bioinformatics 5 08-02-2012 12:23 AM
Pipeline for de novo RNA sequencing, and Galaxy LizBent Bioinformatics 3 05-08-2012 06:41 PM
cufflinks/gencode pipeline issues gcoppola Bioinformatics 0 04-09-2012 04:54 PM

Reply
 
Thread Tools
Old 08-28-2014, 06:20 PM   #1
lucasmiguel
Junior Member
 
Location: Brazil

Join Date: Jul 2014
Posts: 9
Default Best way to compare DEG between de novo pipeline and Cufflinks pipeline

Hi!

I would like to know your opinion about WHAT IS THE BEST WAY to compare DEG ( Differentialy Expressed Genes) between de novo pipeline ( Trinity ->RSEM(bowtie)-> EdgeR or DESeq ) and Cufflinks pipeline (Cufflinks -> TopHat -> Cuffmerge -> Cuffdiff ).

I know that the output of de novo pipeline is in isoforms level. How I can compare this result with DEGs of Cuffdiff ?

I can do a Blast to make a link between each transcript, but in gene levels, how i do it ?
Clustering ?

Thanks to all.
lucasmiguel is offline   Reply With Quote
Reply

Tags
cufflinks, de novo, deg, pipeline, trinity

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 08:58 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO