Repeats integration

Integration and statistics of repeat annotaion

Data prepareing

Four GFF files from repeat annotations: denovo.gff, trf.gff, repeatmasker.gff, proteinmask.gff
A genome File: Genome.fa

merge the overlaps among all the repeats

cat denovo.gff trf.gff repeatmasker.gff proteinmask.gff > all.gff
perl merge_overlap.pl all.gff >merge_overlap.gff

classify each kind of repeats

cat denovo.gff repeatmasker.gff proteinmask.gff > all_without_trf.gff
perl stat.pl -denovo -trf -repeatmasker -proteinmask Genome.fa