TagPileup antisense off by 1bp
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The following composites from TagPileup are of test data where the sense strand is showing the expected line values. The antisense strand is not showing the same line values as the sense based on what the alignments look like in IGV. This off-by-1bp effect is independent of the BED coordinate interval strand/direction and bp window size. This effect is also observed in the matrix output.
BED intervals:
chr12 273959 273969 YLR069C 8 -
chr16 364888 364898 YPL097W 49 +
Test BAM reads:
chr12:273883-273924,+|chr12:273933-27396
chr12:273884-273925,+|chr12:273934-27396
chr12:273885-273926,+|chr12:273935-27396
chr12:273886-273927,+|chr12:273936-27396
chr12:273923-273964,-|chr12:273883-27391
chr12:273924-273965,-|chr12:273884-27391
chr12:273925-273966,-|chr12:273885-27391
chr12:273926-273967,-|chr12:273886-27391
chr12:273963-274004,+|chr12:274013-27404
chr12:273964-274005,+|chr12:274014-27404
chr12:273965-274006,+|chr12:274015-27404
chr12:273966-274007,+|chr12:274016-27404
chr16:364811-364852,+|chr16:364861-36489
chr16:364812-364853,+|chr16:364862-36489
chr16:364813-364854,+|chr16:364863-36489
chr16:364814-364855,+|chr16:364864-36489
chr16:364851-364892,-|chr16:364811-36484
chr16:364852-364893,-|chr16:364812-36484
chr16:364853-364894,-|chr16:364813-36484
chr16:364854-364895,-|chr16:364814-36484
chr16:364891-364932,+|chr16:364941-36497
chr16:364892-364933,+|chr16:364942-36497
chr16:364893-364934,+|chr16:364943-36497
chr16:364894-364935,+|chr16:364944-36497
This fix appeared to reveal a strand-specific shift in the composites (same data):
