Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Read counts from SAM file mapped to de novo assembled transcripts using HTSeq-count alan_sm RNA Sequencing 2 06-12-2015 08:54 PM
TopHat2 failed to read known junctions from GTF file (from ensembl or UCSC) Alex234 RNA Sequencing 4 08-05-2013 08:31 AM
read counts without gff3 file cyendrek Bioinformatics 2 03-05-2013 01:16 PM
cufflinks won't read my GTF file moriah Bioinformatics 0 08-28-2011 12:31 AM
DESeq: Read counts vs. BP counts burkard Bioinformatics 0 08-05-2010 11:52 PM

Thread Tools
Old 01-21-2014, 07:13 PM   #1
Junior Member
Location: RI

Join Date: Nov 2013
Posts: 5
Default GTF file for read counts


I try to get the read counts for gene differential expression analysis using the following command:

htseq-count -m intersection-strict –stranded=no testsort.sam gene.gtf > testsort.counts

Can you tell me what kind of "gene.gtf' file I should use? I used ABySS(de novo assembly) for my transcriptome assembly so it seems I haven't the available reference genome.

I appreciate your help!
witty 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 08:11 PM.

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