I cannot see any description of output files in the documentation (sorry id I have missed it). I am trying to find any tabular output of haplotig / duplication / repeat sequences. The .bed file will state e.g. 'haplotig' but some lines do not state which contig is the 'priamry' and which is the haplotig. Also some lines only have one sequence named - see below.
Hi,
I cannot see any description of output files in the documentation (sorry id I have missed it). I am trying to find any tabular output of haplotig / duplication / repeat sequences. The .bed file will state e.g. 'haplotig' but some lines do not state which contig is the 'priamry' and which is the haplotig. Also some lines only have one sequence named - see below.
ptg003614l 0 31273 HAPLOTIG ptg003121l ptg003586c 0 19692 HAPLOTIG ptg003333l ptg003490l 0 24361 HAPLOTIG ptg003107l ptg003464l 0 43549 HAPLOTIG ptg002158l ptg003156l 0 30804 HAPLOTIG ptg002440l ptg002810l 0 22754 HAPLOTIG ptg002601l ptg002439l 1 46383 HAPLOTIG ... ptg000896l 1325855 3071313 OVLP ptg000425l ptg004326l 1 18766 HAPLOTIG ptg004325l 1 19844 HAPLOTIG ptg004304l 0 25519 HAPLOTIG ptg001289l ptg004111l 1 24637 HAPLOTIG ptg003961l 1 28070 HAPLOTIG ptg003828l 1 28258 HAPLOTIG