SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Could GSNAP results be analyzed by Cufflinks? aquleaf Bioinformatics 2 03-07-2012 09:12 AM
cufflinks 1.2.0 version got me significantly different results than the old version slowsmile Bioinformatics 9 02-01-2012 01:26 AM
Cufflinks cufflinks v1.0.3 - segmentation fault bias correction chrNT annotations adrian Bioinformatics 0 06-08-2011 01:28 PM
Is it normal for cufflinks produce different results in multiple run superligang Bioinformatics 3 03-03-2011 01:40 AM
question about cufflinks results jiexiong Bioinformatics 1 11-17-2010 03:38 PM

Reply
 
Thread Tools
Old 08-16-2011, 10:20 PM   #1
fangquan
Member
 
Location: Boston

Join Date: Jul 2011
Posts: 18
Default cufflinks results

I'm wondering what the results of cufflinks mean.

This is how they explaned:

In the transcripts.gtf, each row represents either a transcript or an exon within a transcript.

The isoforms.fpkm_tracking contains the estimated isoform-level expression values in generic FPKM.

The genes.fpkm_tracking contains the estimated gene-level expression values in the generic FPKM

I noticed two interesting things. (1) in the transcripts.gtf, there is a FPKM value which is from the isoforms.fpkm file and (2) All the entries from isoform.fpkm exist in transcripts.gtf. But exons may exist in several transcripts.

I don't know how the cufflinks exactly work but i guess, it assemble out all the possible transcripts in isoform tracking and exons in gene tracking, and list their composition relations in the transcripts.gtf file.


This is what I understand about cufflinks results, I warmly welcome any comments and discussions.

fangquan
fangquan 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 02:35 AM.


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