SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
cufflinks diffGenes<-getGenes(cuff,diffGeneIDs) error ckrna Bioinformatics 6 12-10-2013 12:43 PM
Uploading XLOC gene IDs to IPA fozturk Bioinformatics 2 05-31-2012 05:04 AM
Extract snp ids seq_GA Bioinformatics 0 11-22-2011 05:09 PM
interpreting gene/transcript names from UCSC table browser human all_mrna Kotoro Bioinformatics 1 10-18-2011 09:42 AM
IDs, standard format? EGrassi Bioinformatics 2 02-28-2011 05:33 AM

Reply
 
Thread Tools
Old 06-02-2012, 04:04 PM   #1
ftan
Junior Member
 
Location: Los Angeles

Join Date: May 2012
Posts: 1
Default Cuff gene and transcript IDs

I'm new to RNA seq and I hope someone can give me some general insight into my cuffcompare output.

My Question: Why are there are multiple cuff_gene_id and cuff_id per reference transcript? I'm trying to extract a single FPKM value per reference transcript, so I don't know how to treat multiple entries for a single gene. For example, my cuffcompare output contains multiple lines for Map4k4:

Map4k4 Map4k4 c CUFF.155 CUFF.155.1 100 569.106817 284.553408 853.660225 378.272059 91 CUFF.155.1 5782
Map4k4 Map4k4 c CUFF.156 CUFF.156.1 100 373909.473540 166501.815197 581317.131882 248528.926936 38 CUFF.156.1 5782
Map4k4 Map4k4 i CUFF.157 CUFF.157.1 100 870264.340261 319860.843931 1420667.836591 578444.457660 37 CUFF.157.1 5782
Map4k4 Map4k4 i CUFF.158 CUFF.158.1 100 870264.340261 319860.843931 1420667.836591 578444.457660 37 CUFF.158.1 5782

Are these individual fragments that have been mapped to Map4k4 with an associated FPKM? If so, is the FPKM for Map4k4 just the sum of individual entries? Sorry, I'm new...
ftan 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 04:08 PM.


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