Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Using htseq-count with paired-end and orphaned reads roloman Bioinformatics 5 09-17-2013 04:46 PM
HTseq-count : how to get unique reads? ThePresident Bioinformatics 11 08-19-2013 05:11 PM
[HTSeq-Count] How are reads counted? syintel87 Bioinformatics 0 06-17-2013 02:18 PM
Reads Count - HTSeq alternative? NGSAwesome RNA Sequencing 1 10-15-2012 10:13 AM
htseq-count gets more reads? deepsea Bioinformatics 3 03-29-2012 12:27 PM

Thread Tools
Old 10-02-2014, 05:02 AM   #1
Junior Member
Location: Tel Aviv, Israel

Join Date: Oct 2014
Posts: 1
Default HTSeq - paired reads count

I was wondering if there were any changes in the latest version on HTSeq (after Version 0.5.4) that could affect the count of paired reads (other than what's mentioned in the documentation)?
I have a test dataset which I tested a few months ago (before the version update) and I see that the new version gives slightly different results (about 10% of the genes's counts have changed).
Based on the documentation, the only change that could possibly affect the counts is the default for parameter minaqual, but I ran the new version with a=0 (which was the default in the previous version) and there was still a difference in the counts. What else could be affecting this? I haven't changed anything in the dataset or in the parameters/versions of other programs (same version of tophat, same GTF file etc.)
nofar is offline   Reply With Quote

htseq, htseq count, htseq-count

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 06:09 PM.

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