SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
htseq-count failure parsing GFF attribute line pshah Bioinformatics 1 12-03-2015 01:22 AM
Error in htseq-count diego diaz Bioinformatics 4 04-08-2015 01:02 AM
Error with GTF file when using htseq-count MDonlin Bioinformatics 13 01-13-2015 08:29 AM
Error when using HTSeq count shocker8786 Bioinformatics 2 02-19-2014 10:10 PM
htseq-count error sissi Bioinformatics 0 03-20-2012 11:40 PM

Reply
 
Thread Tools
Old 05-27-2016, 12:37 PM   #1
OxytocinHeadHunter
Junior Member
 
Location: Barcelona

Join Date: Apr 2016
Posts: 3
Question htseq-count ERROR in GFF File?

Hello guys,

I'm trying to do a summary of counts in usegalaxy.org. I convert Fatq groomer to sam with Map with BWA for Illumina (Galaxy Version 1.2.3) with a camponotus floridanus genome and
now i have a sam file:

~98,000,000 lines, 24,027 comments
format: sam database?
BWA Version: 0.5.9-r16 BWA run on single-end data



And a gff3 file from http://hymenopteragenome.org/campono...tium_datasets:

~190,000 lines
format: gff3 database?
uploaded gff3 file

When i do a summary of counts with htseq-count:

Fatal error: Unknown error occured
Error occured when processing GFF file (line 5 of file /galaxy-repl/main/files/016/000/dataset_16000531.dat):
Feature CFLO10001-RA does not contain a 'gene_id' attribute
[Exception type: ValueError, raised in count.


Thanks you everyone!
OxytocinHeadHunter is offline   Reply With Quote
Reply

Tags
bioinformatics help, gff, htseq-count, summary of counts, usegalaxy

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 11:54 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO