Hello,
I am trying to use GViz for plotting genes annotations from GTF/GFF files.
It works nicely with files downloaded from UCSC table browser (refflat, refseq, gencode). However I could not find a way to download a file that provides simultaneous genes and transcripts information. All the lines share the same 'gene_id' and 'transcript_id'.
When I download annotations directly from gencode website, it seems that these file carry more information (genes/transcripts/symbols...) : http://www.gencodegenes.org/releases/current.html
However, while the latter ones are correctly loaded and parsed by the constructor 'GeneRegionTrack', the plotting step does not resolve the internal gene structure (just a big box, no exons or thin boxes for non coding...). I tried playin with the thinBoxFeature in vain.
Has anybody experience the same ?
Using the gencode files would be very helpful because it allows to use ensembl IDs or genes symbol directly for selecting genes/transcripts. My question probably reflects my misunderstanding of UCSC/Gencode or GFF/GTF file formats. Any help would be appreciated :)
On a side question, is GViz package still maintained ? Or should I ask my questions about it on a more adapted forum/list ?
Thank you for your help.
Romain.