Converting TOGA results into different formats

Parent page - Interpreting results

(https://github.com/hillerlab/TOGA/issues/56) TODO: check whether the issue is documented

TOGA's bed file - query_annotation.bed

TOGA saves the resulting annotation into a bed-12 formatted file.

Bed to Gff

bedToGenePred query_annotation.bed stdout | genePredToGtf stdin query_annotation.gtf

genePredToGtf has some options that could be useful. genePredToGtf - Convert genePred table or file to gtf.

usage:
genePredToGtf database genePredTable output.gtf
If database is 'file' then track is interpreted as a file
rather than a table in database.
options:
-utr - Add 5UTR and 3UTR features
-honorCdsStat - use cdsStartStat/cdsEndStat when defining start/end
codon records
-source=src set source name to use
-addComments - Add comments before each set of transcript records.
allows for easier visual inspection
Note: use a refFlat table or extended genePred table or file to include
the gene_name attribute in the output. This will not work with a refFlat
table dump file. If you are using a genePred file that starts with a numeric
bin column, drop it using the UNIX cut command:
cut -f 2- in.gp | genePredToGtf file stdin out.gp