Hello list members, 

For a RNA-seq analysis, what would you suggest to use to convert raw-sequence-based read coverage to annotated ORF-based coverage, if the genome of interest is NOT supported in neither UCSC nor ENSEMBL, which means that creation of a TranscriptDB object in a straightforward way (I.e. according to the GenomicFeatures pipeline) is impossible? What would you recommend to import a .gff file (containing annotation of a particular genome, from GenBank) into R/Bioconductor to eventually generate a gene-centric countTable readable by packages like DESeq?

Thank you!

Oleg

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