Blacklists

Install the bundled blacklist BED files:

sjcab-peak2anno-db install-blacklists
sjcab-peak2anno-db install blacklists

Outputs are stored as {db-path}/blacklists/{name}.bed. For provenance and source details, see the bundled blacklist notes.

Resource URLs

• Boyle Lab blacklist lists
• ENCODE blacklist annotation
• Kundaje ENCODE blacklist notes

Liftover comparison

The following is an interval-overlap comparison of the generated liftover files against the native target blacklist files:

• TP: native truth intervals with at least one base overlapping a liftover interval.
• FN: native truth intervals without an overlap (native truth - TP).
• TPR = TP / native truth; FNR = FN / native truth.
• merge is applied to the liftover result before overlap testing. none means sorted but unmerged input; the other values are bedtools merge -d N.

assembly	liftover	merge	native truth	liftover intervals	TP	TPR	FN	FNR
hg19	CrossMap	none	1,871	59,857	1,426	76.216%	445	23.784%
hg19	CrossMap	100	1,871	7,713	1,426	76.216%	445	23.784%
hg19	CrossMap	200	1,871	6,575	1,426	76.216%	445	23.784%
hg19	UCSC liftOver	none	1,871	2,237	1,255	67.076%	616	32.924%
hg19	UCSC liftOver	100	1,871	2,186	1,255	67.076%	616	32.924%
hg19	UCSC liftOver	200	1,871	2,158	1,255	67.076%	616	32.924%
mm10	CrossMap	none	4,874	270,480	64	1.313%	4,810	98.687%
mm10	CrossMap	100	4,874	5,478	64	1.313%	4,810	98.687%
mm10	CrossMap	200	4,874	4,828	64	1.313%	4,810	98.687%
mm10	UCSC liftOver	none	4,874	232	3	0.062%	4,871	99.938%
mm10	UCSC liftOver	100	4,874	69	3	0.062%	4,871	99.938%
mm10	UCSC liftOver	200	4,874	68	3	0.062%	4,871	99.938%

Prediction-side overlap

If the question is “how many liftover regions overlap native truth?”, the corresponding metric is prediction precision/positive predictive value (PPV), not TPR. Here liftover TP is a liftover interval overlapping at least one native truth interval, and liftover FP is a liftover interval with no native overlap. The native-truth recall columns are retained for reference.

assembly	liftover	merge	liftover intervals	liftover TP	PPV	liftover FP	native TP	native TPR
hg19	CrossMap	none	59,857	47,262	78.958%	12,595	1,426	76.216%
hg19	CrossMap	100	7,713	3,286	42.603%	4,427	1,426	76.216%
hg19	CrossMap	200	6,575	2,773	42.175%	3,802	1,426	76.216%
hg19	UCSC liftOver	none	2,237	1,342	59.991%	895	1,255	67.076%
hg19	UCSC liftOver	100	2,186	1,329	60.796%	857	1,255	67.076%
hg19	UCSC liftOver	200	2,158	1,329	61.585%	829	1,255	67.076%
mm10	CrossMap	none	270,480	4,487	1.659%	265,993	64	1.313%
mm10	CrossMap	100	5,478	150	2.738%	5,328	64	1.313%
mm10	CrossMap	200	4,828	134	2.776%	4,694	64	1.313%
mm10	UCSC liftOver	none	232	4	1.724%	228	3	0.062%
mm10	UCSC liftOver	100	69	4	5.797%	65	3	0.062%
mm10	UCSC liftOver	200	68	4	5.882%	64	3	0.062%

Confidence and limitations

These figures are overlap-based recall only. They do not measure false positive intervals, coordinate accuracy, one-to-many mappings, or whether the liftover output retains the intended blacklist boundaries. The very large CrossMap interval counts, particularly for mm10, indicate fragmentation or one-to-many mappings and should not be interpreted as higher confidence. The mm10 blacklist results have extremely low recovery with both methods and should be treated as unsuitable without additional review against a native mm10 blacklist release. Results can also change with the selected chain file, input release, chromosome naming, and merge policy.