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Old 10-18-2013, 01:44 AM   #1
bernardo_bello
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Location: Spain

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Smile Is this a valid GFF3 file for HTSeq?

Hi there,

I created a gff3 file from GenBank file containing multiple contigs (using Bioperl 'genbank2gff3.pl' tool) . In order to run HTSeq I removed the ##FASTA section (HTSeq doesn't likes). My gff3 file is missing the headers at the start of the file but HTSeq seems doesn' t mind.

I have a result from HTSeq but I'm not sure I did something wrong.

GFF3 file is attached.

Thank you for your help.

Best, Bernardo

python -m HTSeq.scripts.count -m intersection-nonempty -t CDS -i ID R_2012_09_17_05_52_53_user_PGM-18-BB_Auto_PGM-18-BB_19_2.sam HPNK.gbf.gff > HPNK_2.counts


https://github.com/bioperl/bioperl-l...enbank2gff3.pl
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Old 10-18-2013, 01:46 AM   #2
bernardo_bello
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https://docs.google.com/file/d/0B8-Z...it?usp=sharing
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