OUTRIDER RNASeq Gencode annotation

Question

[omicsnstuff]

I'm assessing the utility of outrider for RNASeq diagnostics.

My count table is generated using the gencode annotation I'm not sure how to set this up as an object which I can use in the OUTRIDER syntax for pre-processing steps.

I'm a relative novice with R and am running through Linux OS.

I have the GTF file saved, but am uncertain how I then use this as the framework for my pre-processing steps, as opposed to the UCSC hg19 element found i the manual.

can someone advise?

Answer 1

[felix.brechtmann]

Hi, it should simply work when you pass the file path of the gtf file instead of the txdb object to the filter function.

Please let us know, in case this doesn't work.