Howto Collapse Multiple Exonerate Gff Into One Gene Prediction Set
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,
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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
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