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<div>htseq-count doesn’t support GFF3, only older GFF or GTF (note the ‘gene_id’ attribute is very much a GTF thing). I mention this here (and the reasons why you should be wary):</div>
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<div> <a href="http://www.biostars.org/p/83903/">http://www.biostars.org/p/83903/</a></div>
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<div>In short, don't trust htseq-count results (particularly for any eukaryotic counts) unless you convert to a supported format. This is pretty easy to do, actually; the gff_read tool that comes with Cufflinks does a decent job, and there are other tools
capable of doing the same. Also be aware that if you use PE alignments the BAM file must be name-sorted, not coordinate-sorted.</div>
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<div>Also, just to point out, there is a much faster C-based multithreaded alternative to htseq-count called featureCounts that takes one or more native BAM files as input (it unfortunately doesn’t support GFF3 either). Results are pretty much identical to
htseq-count.</div>
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<div>chris</div>
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<div>On Feb 28, 2014, at 7:42 PM, Hans Vasquez-Gross <<a href="mailto:havasquezgross@ucdavis.edu">havasquezgross@ucdavis.edu</a>> wrote:</div>
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<div>Hi All,</div>
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<div> I just wanted to also point out another standard gff parsing tool isn't able to work with your gff3 reference with the following error highlighted in bold:</div>
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<div> samtools view -sB Kronos0_KTC1_bwa_ABgenome_20131211.sorted.rmdup.bam | htseq-count - /Volumes/DATA2/users/havasquezgross/Projects/exon_capture/database/Triticum_aestivum.IWGSP1.21.noQs.gff3</div>
<div>Error occured in line 137 of file /Volumes/DATA2/users/havasquezgross/Projects/exon_capture/database/Triticum_aestivum.IWGSP1.21.noQs.gff3.</div>
<div><b>Error: Feature Traes_3AS_775C097A2.E1 does not contain a 'gene_id' attribute</b></div>
<div>[Exception type: SystemExit, raised in count.py:55]</div>
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<div>Another item to consider for the march release. I look forward to working with the updated release.</div>
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<div>Cheers,</div>
<div>-Hans</div>
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