PAPerFly: Partial Assembly-based Peak Finder for ab initio binding site reconstruction

BMC Bioinformatics

Table 3 Results of the PAPerFly chiptigs and peaks analysis from human experiments ChIP-seq

Ident	Read	Chiptigs	Chiptigs	Chiptigs	Chiptigs	Peaks
Ident	Length	\(\ge\) k	\(\ge\) 1.1 k	\(\ge\) 1.25k	\(\ge\) 1.5k	Peaks
ENCFF000QLL	50	0.792559	0.503727	0.292983	0.179104	0.611732
ENCFF000VPU	36	0.441083	0.201490	0.113473	0.058234	0.910155
ENCFF000WDW	36	0.383082	0.191694	0.118622	0.058065	0.931330
ENCFF000XML	36	0.747459	0.528556	0.373114	0.264857	0.836959
ENCFF000YOW	27	0.590401	0.398515	0.386667	0.285714	0.064128
ENCFF000ZBR	36	0.865953	0.723484	0.553480	0.403001	0.807809
ENCFF002EDN	36	0.507555	0.279538	0.193993	0.108176	0.793017
ENCFF002ELA	100	0.090052	0.000000	0.000000	0.000000	0.177778
ENCFF156EZY	100	0.745610	0.649912	0.451807	0.269036	0.612676
ENCFF263VVK	100	0.733179	0.815248	0.668945	0.537217	0.815476
ENCFF424HPQ	100	0.269091	0.336207	0.400000	0.500000	0.157895
ENCFF489ABL	100	0.812528	0.805628	0.645051	0.502525	0.867299
ENCFF793WFY	100	0.889042	0.925232	0.845278	0.779911	0.984674
ENCFF903KXG	100	0.765208	0.914712	0.829531	0.797917	0.989831

In each of the columns, there is the portion of the PAPerFly chiptigs (or peaks) that match a peak sequence as is found by standard peak-calling methods. Only the chiptigs that match a standard peak from at least 75% are counted. For long-read experiments ENCFF002ELA and ENCFF424HPQ and for the short-read experiment ENCFF000YOW, less than 20 PAPerFly chiptigs longer than 1.5k were found. For other long-read experiments, lower thousands of chiptigs were reconstructed. Peaks were reconstructed only from chiptigs longer than 1.25k

ISSN: 1471-2105