Apparently I need to use a gtf or gff3 file for annotation with easyRNAseq now when processing hg19 bamfiles now - as method biomaRt uses GRCh39 and I get an error. So far so bad.
However, I seem not to be able to download a gtf or gff3 file for hg19 that easyRNAseq would accept:
> DGE<-simpleRNASeq(bamFiles=getBamFileList(bamfiles), param=param, nnodes=4, verbose=T, override=T)
Processing the annotation
Validating the annotation source
Read 993 records
Error in .validate(obj, verbose = verbose) :
The provided gff3 contains no annotation of type 'mRNA' and/or 'exon' in the first 1000 lines.
I've tried files the following annotation files but none seems to work:
will try the Illumina iGenome next. What am I missing here?!?