Table 2. Sequencing reads statistics for some genome-wide CLIP studies.

Experiment	# Total sequencing reads (million by default)	# Unique sequencing reads (million by default)	# Uniquely mapped reads (million by default)	# Replicate	Method to handle replicates	Year	Citation
HITS-CLIP	26 (all replicates combined)	∼1.8 of all mapped reads	Unclear whether mapping allows non-unique alignment	5	Biologic complexity	2009	(26)
PAR-CLIP	4.1–33 (all replicates combined)	0.65–7.0	20–70% of sequencing reads after adaptor removal	1–7	Pooled	2010	(38)
iCLIP	6.5 (all replicates combined)	0.6 out of 4.2M uniquely mapped reads	4.2	3	Pooled	2010	(39)
PAR-CLIP	22–24 (all replicates combined)	Not reported	2.6–4.1	2	Pooled	2011	(15)
iCLIP	113 (all replicates combined)	33 out of 43M uniquely mapped reads	43	3	Focus on binding sites reproduced in all replicates	2012	(40)
HITS-CLIP	36–37 (second replicate)	0.95–1.5 out of 11M–15M uniquely mapped reads	11–15	2	Analyze the second replicate	2012	(36)
PAR-CLIP	60 (all replicates combined)	1.1	0.32	4	Pooled	2013	(37)
HITS-CLIP	72	0.35	0.22 out of 0.35M unique sequencing reads	1	NA	2014	(42)
HITS-CLIP	250–340 (each protein)	0.87–2.3	Not reported	4–5	Pooled	2014	(43)
iCLIP	169–433 (all replicates combined)	0.16–9.6 out of all mapped reads	12–48%	2	Pooled	2015	(41)