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Old 03-07-2013, 08:37 AM   #1
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Location: New Mexico

Join Date: Nov 2009
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Default How do you get the gene length that htseq-count is using?

Hi, I have human rna-seq data and I'm using htseq-count to get the number of reads that map to Ensembl genes. I believe htseq-count uses a union model to summarize the transcripts into genes. How can I get the either the coordinates of the gene model and/or the length? After htseq-count, I would like to use UPC software ( which requires as input the number of reads mapping to each gene, the length of the gene, and the GC content of the gene.

Thank you for your input.
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