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Old 02-23-2011, 06:05 AM   #1
Matthias
Junior Member
 
Location: Berlin

Join Date: Nov 2010
Posts: 2
Default 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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