Entering edit mode
8.6 years ago
int11ap1
▴
490
I have the following Net file:
##matrix=axtChain 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
##gapPenalties=axtChain O=400 E=30
net chr10 133797422
fill 10813 2915 chr6 + 28183799 3111 id 913 score 185812 ali 2866 qDup 569 type top
fill 13728 142 chr2 - 548670 130 id 14353 score 4742 ali 130 qDup 0 type top
fill 13870 3519 chr6 - 28223593 5985 id 743 score 227296 ali 3424 qDup 647 type top
fill 24561 8076 chr10 + 15726894 3259 id 13370 score 43301 ali 2569 qDup 3089 type top
gap 25731 823 chr10 + 15728467 33
gap 27454 4542 chr10 + 15729394 137
fill 32657 10982 chr7 + 90354424 7122 id 2540 score 92583 ali 2677 qDup 0 type top
gap 33371 8186 chr7 + 90355149 4268
by calling netToBed
to have the aligned regions, I get the following:
chr10 10813 13728
chr10 13728 13870
chr10 13870 17389
chr10 24561 32637
chr10 25731 26554
chr10 27454 31996
chr10 32657 43639
chr10 33371 41557
Why the gaps are included (they are not aligned regions, besides of giving redundant coordinates)?