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Old 06-17-2013, 04:38 PM   #1
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Location: California

Join Date: Feb 2013
Posts: 7
Default dexseq aggregate genes


I'm trying to understand the "-r no" option in the latest version of It seems that the script only ignores an exonic part if it exactly overlaps an exonic part from another gene - is this correct? Couldn't gene-level differential expression also disrupt differential exon usage calls if an exonic part of one gene is a subset of an exonic part of another?



E.g. here are some lines from running the script on gencode 14 annotation. The first exonic part contains the subsequent ones and more (from a different gene), so I'm wary when DEXSeq tells me it's used differentially.

chr19 aggregate_gene 2252252 2269758 . - . gene_id "ENSG00000167476.5"
chr19 exonic_part 2269408 2269758 . - . transcripts "ENST00000593238.1"; exonic_part_number "012"; gene_id "ENSG00000167476.5"
chr19 aggregate_gene 2269519 2273487 . + . gene_id "ENSG00000104904.6"
chr19 exonic_part 2269519 2269519 . + . transcripts "ENST00000583542.2+ENST00000582888.2"; exonic_part_number "001"; gene_id "ENSG00000104904.6"
chr19 exonic_part 2269520 2269528 . + . transcripts "ENST00000583542.2+ENST00000322297.4+ENST00000582888.2"; exonic_part_number "002"; gene_id "ENSG00000104904.6"
chr19 exonic_part 2269529 2269529 . + . transcripts "ENST00000583542.2+ENST00000581150.1+ENST00000582888.2+ENST00000322297.4"; exonic_part_number "003"; gene_id "ENSG00000104904.6"
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