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  • shambo
    Junior Member
    • May 2012
    • 6
    #1

    Cuffdiff parameter regarding minimum reads within locus

    Hi all,

    I have two RNAseq samples which I've tophat'ed and have BAMS for. I'm trying out cuffdiff using a refseq GTF file.

    The question is, if this param is set to 1000 for example, will it detect genes where in one sample the gene is expressed, but not expressed at all in the other sample? Or would it exclude a gene like this being testing because both loci do not exceed 1000 reads?

    Suggestions for this parameter would be useful too. The 1000 default in Galaxy seems way too high.

    Any help appreciated. TIA

    Sham
    Tags: cuffdiff, differential expression, minimum reads
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