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Old 01-17-2018, 11:08 AM   #1
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Location: Saint Louis

Join Date: May 2014
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Default HTSeq and repeated exons

Does anyone know how htseq-count handles reads that map to an exon that is found in two alternative transcripts of the same gene? That exon will be repeated twice in a GFF file (once for one transcript and once for the other transcript). Will HTSeq assign two read counts to the corresponding gene for each read that maps to that exon, since that exon is represented twice in the GFF file? Or will HTSeq assign only one read count to the corresponding gene for each read that maps to that exon, since it is the same exon just repeated twice in the GFF file?

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alternative transcript, exon, htseq count, rna-seq

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