Go Back   SEQanswers > Applications Forums > RNA Sequencing

Similar Threads
Thread Thread Starter Forum Replies Last Post
Removing overlapping genes from annotation for RNAseq read count DRAT Bioinformatics 2 04-11-2014 03:53 AM
How do I get a genes.gtf file for RNA Seq Analysis jmwhitha Bioinformatics 8 06-20-2013 12:13 PM
RNASeq paired-end strand specific attribute location in FASTA file mknut Bioinformatics 2 12-06-2012 08:44 AM
Single end RNAseq- no BAM file generated ibn.adam RNA Sequencing 0 10-28-2011 06:53 AM
Errors in cuffdiff genes.fpkm_tracking file kmcarr Bioinformatics 0 05-27-2010 09:18 AM

Thread Tools
Old 10-18-2013, 03:34 AM   #1
Location: Maryland

Join Date: Apr 2010
Posts: 31
Default RNAseq Genes Different By File


I have diff files from ~20 different RNA sequencing experiments. A common GTF file was utilized to make these diff files. The number and identity of the genes in the diff files is different in each file. Some genes overlap but some do not. My question is:

If a gene is not present in the diff file but was present in the GTF file does that mean it is not expressed?

Any clarification is greatly appreciated.
nexgengirl is offline   Reply With Quote
Old 10-18-2013, 04:19 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

It kind of depends on how the "diff files" were made. It could be that only significantly DE genes were written, or that these genes were just filtered out in some experiments, or something else entirely. Even if they were filtered out, I wouldn't necessarily take that to mean the genes aren't expressed, just that they didn't produce enough signal to be useful (assuming there was filtering done and, if so, done properly).
dpryan is offline   Reply With Quote

diff, gtf, rna, rnaseq, sequencing

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 05:22 AM.

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