AlgoLab/PIntron — Issue #9: Producing GTF files that can be uploaded to the UCSC Genome Browser
Author: yp
Created: 2011-12-14 17:29:39+00:00
State: open

Currently PIntron produces two GTF files (by default) to describe the predicted full-length isoforms.
The GTF files are (mostly) standard-compliant but cannot be directly uploaded to the [UCSC Genome Browser](http://genome.ucsc.edu/cgi-bin/hgGateway) since the features' coordinates (fields 4 and 5) are relative to the input genomic sequence and not absolute.
The FASTA header of the genomic sequence contains all the information (chromosome, sequence start and end position, and sequence strand) for reconstructing the absolute coordinates.

I would suggest that PIntron should produce a GTF file where the features' coordinates are absolute and not relative (or, at least, to introduce a flag that allows to obtain such a file).