[ensembl-dev] GFF file into Gbrowse

[Sung Gong]

Hi,

I was wondering whether the coordinates from GTF file of Ensembl
(ftp://ftp.ensembl.org/pub/current/gtf/homo_sapiens/) are compatible
with the FASTA sequence from UCSC
(http://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/).

What I want to do is to display short reads from the Solid4 platform
using Gbrowse2.0. The read mapping and pairing were done based on the
fasta file of UCSC hg_19 without masking repeat options.

Also wondering the coordinates of the GTF are based on repeat-masking or not?

The GTF file was converted into GFF file from the sequence ontology
website (http://www.sequenceontology.org/cgi-bin/converter.cgi).

Where do you usually download FASTA and GFF files to display your short reads?

Cheers,
Sung