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Old 04-12-2012, 02:50 AM   #1
Location: Milano, Italy

Join Date: Aug 2011
Posts: 92
Default DEXSeq exonic_part_number

Dear All,
I am a bit confused about flattening gtf file to prepare raw counts to use with DEXSeq R package,
I run both pyhton scripts included in the package and start to anaylze my data with R,
I don't understand what does exonic_part_number means for in the gff flattened file, for instance if I have a gene with 8 exons why I obtain in the gff file 20 exonic_part_numbers?
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Old 04-12-2012, 08:40 AM   #2
Simon Anders
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Location: Heidelberg, Germany

Join Date: Feb 2010
Posts: 993

Please see Figure 1 of our paper, which should explain this. Note that, in the paper, we use the term "counting bin" rather than "exonic part". (Sorry for this inconsistency.)
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