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.

Rosenkranz and Zischler BMC Bioinformatics 2012 13:5   doi:10.1186/1471-2105-13-5