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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
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