Howto Collapse Multiple Exonerate Gff Into One Gene Prediction Set

Question

[Leszek]

Hi there,

I've quite general question about gene prediction/gff. I've mapped homologous sequences from close genomes onto my assembly with exonerate and now I would like to get one gff with collapsed/unified information. Do you know any program, or maybe you're in possesion of script to do it?

Cheers,

Answer 1

[Kamil]

Sounds like you should try BEDTools by Aaron Quinlan. The programs can handle BED, GFF/GTF, VCF, and SAM/BAM files.

Since you want to "collapse" the annotations, try mergeBed. Here's a tiny example:

$ cat mergeBed_example.bed
chr1    1   10  other stuff
chr1    5   15  more stuff
$ mergeBed -i mergeBed_example.bed
chr1    1   15