proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis

BMC Bioinformatics

Table 2 Detection of human, mouse and rat piRNA clusters using proTRAC with different thresholds

species	thresholds^*	minimum piRNA density [hits/kb]^**	minimum loci/cluster	cluster candidates	tracked clusters (mono-, bi-, non-directional)^***	p 0/≥2 mistakenly annotated clusters
	0.05/1.3	0.1 - 1.4	6	25402	368 (202, 120, 46)	0.001/0.992
human	0.01/2.0	0.6 - 2.4	8	14381	187 (139, 40, 8)	0.700/0.049
	0.001/3.0	1.5 - 3.5	11	4558	119 (99, 19, 1)	0.984/<0.001
	0.05/1.3	1.5 - 2.3	6	57260	242 (163, 63, 16)	0.133/0.595
mouse	0.01/2.0	2.5 - 3.4	8	51332	171 (129, 38, 4)	0.866/0.009
	0.001/3.0	3.7 - 4.7	11	37403	151 (123, 25, 3)	0.988/<0.001
	0.05/1.3	1.2 - 1.7	6	34069	186 (139, 43, 4)	0.334/0.293
rat	0.01/2.0	1.8 - 2.7	8	36402	168 (138, 28, 2)	0.926/0.003
	0.001/3.0	2.8 - 3.7	11	28576	162 (136, 26, 0)	0.994/<0.001

*Significance level for increased hit density/minimum score for strand bias, enrichment of loci corresponding to infrequently mapped reads and enrichment of putative piRNA loci with 1T/10A. **depending on chromosomal piRNA density. ***mono-, bi-directional: >75% of mapped sequences located on the main strand.

ISSN: 1471-2105