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  • ERANGE-RNASeq with ensemble annotation

    Hi,

    I'm comparing different RNA Seq analysis pipelines, therefore I want to use ERANGEv3.21 with ensemble annotations, but I'm struggling with the manual.
    I managed to build the extended genome, mapped the reads with bowtie and created a rds file from it.
    Then i counted the unique reads with the <-models gff-file> option, but in the output file where no ensemble gene ids but gene symbols (which where not given in the gff file).
    When counting the splice junction reads, there where only 0 counts.

    Unfortunately the manual is very sparse at this point. Do you have experience with that matter?

    Thanks, Matthias

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