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+bwakit
+=======
+
+Written by Guy Bottu for the GenePattern server of VIB BioinforlmaticsCore,
+takes as input a GTF file and writes a BED file in 12 column format
+with information about transcripts, for use with RSeqC.
+
+The "thick" information is about the coding region, ideally it goes from
+start codon to stop codon, but is information is lacking (e.g. because
+of missing sequence or missing annotation), we use the CDS information.
+For some transcripts there are multiple start or stop codons. We amways
+choose the "thick" so that is has maximum length.
+
+If there is no CDS information (as for ncRNA) the "thick" will have just a
+repeat of the transcript start position, as per BED convention.
+
+modified for integration under GenePattern
+
+usage : perl gtf_to_bed.pl <GTF file> <output file>