SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
htseq-count paolo.kunder Bioinformatics 10 10-22-2014 05:45 AM
Which ID should be used for HTSeq-count? syintel87 Bioinformatics 11 02-07-2013 01:16 AM
Issue with htseq-count cpleis Bioinformatics 8 10-15-2012 10:31 AM
multiBamCov or htseq-count to count read per feature ? NicoBxl Bioinformatics 1 07-03-2012 03:05 AM

Reply
 
Thread Tools
Old 03-07-2013, 09:37 AM   #1
jebe
Junior Member
 
Location: New Mexico

Join Date: Nov 2009
Posts: 9
Default How do you get the gene length that htseq-count is using?

Hi, I have human rna-seq data and I'm using htseq-count to get the number of reads that map to Ensembl genes. I believe htseq-count uses a union model to summarize the transcripts into genes. How can I get the either the coordinates of the gene model and/or the length? After htseq-count, I would like to use UPC software (http://jlab.bu.edu/software/scan-upc/) which requires as input the number of reads mapping to each gene, the length of the gene, and the GC content of the gene.

Thank you for your input.
jebe 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 12:10 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO