Fill/Gap in Net format alignments
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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)?

net alignment ucsc • 1.1k views
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