Content Comparison

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/work/projects/BioITeam/common/script/gtf_to_bed.pl sc_genes.gff 1 \
  > sc_genes.converted.bed

The program reads the input file twice – once to gather all the attribute names, and then a second time to write the attribute values in well-defined columns. You'll see output like this:

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To find out what the resulting columns are, look at the header line out the output BED file:

head -1 sc_genes.converted.bed 

For me the resulting 16 attributes are as follows (they may have a different order for you). I've numbered them below for convenience

 1. chrom          2. start   3. end     4. featureType  5. length  6. strand
 7. source         8. frame   9. Alias  10. ID          11. Name   12. Note
13. Ontology_term 14. dbxref 15. gene   16. orf_classification

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