I am using bedtools complement to find the regions not covered in a GFF file.
Genome file is as follows.
GFF file likes below.
chr1 db exon 1 45 . + . ID=gene1 chr1 db exon 90 450 . + . ID=gene2 chr1 db exon 1 30 . - . ID=gene99
I run complementBed -i <gff_file> -g <genome_file> and got the following result.
chr1 45 89 chr1 450 12222
This is not what I expected. I hope to get the following information, which includes strand symbol. Could anyone help? Thank you very much!
chr1 45 89 + chr1 450 12222 + chr1 30 12222 -