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  • DESeq: Read counts vs. BP counts

    Hi Simon,

    is it possible to use raw bp counts (how often a bp is sequenced within a region) of an exon/transcript for differential expression analysis with DESeq?
    First I think, that if we consider the expression of an individual exon the bp count would avoid double counting of split reads (especially if it belongs to a major part to one exon). It would only assign a portion of the read to one exon. Second, it would be nice to use with cufflinks where cov*length = bp count. Also for cufflinks the bp count divided by the read length is not necessarily equal the read count, especially for alternative transcripts or if you provide a gtf of known genes (even though its an approximation).

    Thanks a lot and best regards,
    Thomas

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