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  • MMSEQ/DESeq question

    Hello,
    I am trying to feed MMSEQ estimated counts into DESeq to test for differential expression. I'm currently looking at an F1 hybrid which has been mapped to a concatendated transcriptome of its parents. I used the mmseq.R script to feed in the mmseq files and defined a partition (containing the suffixes corresponding to two different classes of haplotypes - the parents - separated by a "|" character) and am following these general instructions:
    Haplotype, isoform and gene level expression analysis using multi-mapping RNA-seq reads - eturro/mmseq


    Now I'd like to define "cds" for DESeq -- like so, for example: cds = newCountDataSet(round(tab), c("group1", "group1", "group2", "group2") ) -- but I'm not sure how to define my groups at this point given my partioning of the mmseq files by the parents.
    Any ideas?
    I apologize if the answer to this question seems obvious, I'm very new to bioinformatics.
    Thanks for any help!

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