Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
cuffmerge/cuffcompare: result contains no p_id martin_313 Bioinformatics 1 01-12-2012 04:23 AM
what are your thouths about this result nicedad General 2 09-01-2011 02:40 AM
cuffcompare????????? semna Bioinformatics 0 05-15-2011 03:21 AM
Binary characters in cuffcompare result & Questions on cuffdiff nkwuji RNA Sequencing 3 11-03-2010 03:01 AM
To cuffcompare or not to cuffcompare poisson200 Bioinformatics 5 08-08-2010 03:58 AM

Thread Tools
Old 04-16-2010, 12:18 PM   #1
Location: Germany

Join Date: Oct 2009
Posts: 59
Default Cuffcompare Result help

Dear all,

I just run cuffcompare -r [reference.GTF] [transcript.GTF], the output file included the transcripts.tmap which showed gene names and FPKM info. Following is one of the genes:

Bdnf ENSMUST00000053317 = CUFF.114250 CUFF.114250.1 97 32.073177 28.162251 35.984103 35.033306 1633 CUFF.114250.1
Bdnf ENSMUST00000111050 = CUFF.114251 CUFF.114251.2 100 33.063804 27.584704 38.542903 36.115361 1249 CUFF.114250.1
Bdnf ENSMUST00000111052 = CUFF.114252 CUFF.114252.3 62 20.483324 14.448689 26.517959 22.373791 1105 CUFF.114250.1
Bdnf ENSMUST00000111047 c CUFF.114254 CUFF.114254.1 100 10.649808 7.099872 14.199745 11.639716 235 CUFF.114254.1
Bdnf ENSMUST00000111042 c CUFF.114256 CUFF.114256.1 100 23.582192 21.902030 25.262353 25.777043 2323 CUFF.114256.1
Bdnf ENSMUST00000053317 p CUFF.114258 CUFF.114258.1 100 0.557202 0.000000 1.467470 0.609143 187 CUFF.114258.1

I am a bit confused with the result, since I have done qPCR experiment of BDNF gene, and it will be upregulated like 5-6 folds compared with control. I only run with the treated sample and the reference GTF file, so the FPKM value is not the like fold change, right? also the class code, should I only trust "="? and what does "p" and "i" mean? If I only use "=" FPKM value, how can I extract the one with the class code "="?

And if I run cuffcompare -r [reference.GTF] [treated.GTF] [control.GTF], how could I get the fold changes (treated/control)?

Sorry for such naive questions? Can someone kindly explain to me?

With many thanks in advance!!

Wei-HD 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 02:15 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO