Assessing Computational Steps for CLIP-Seq Data Analysis

Table 1

Mapping summary of CLIP, INPUT, and RNAseq reads.  

Sample		Total reads	Aligned reads (%)	Unique aligned reads (%)
Human	Caco2_CLIP_1	34,498,894	12,095,664; (35.1%)	10,977,657; (31.8%)
	Caco2_CLIP_2	33,617,355	12,650,034; (37.6%)	11,514,201; (34.3%)
	Caco2_CLIP_3	48,866,964	17,965,486; (36.8%)	15,502,638; (31.7%)
	Caco2_INPUT_1	26,095,707	4,634,066; (17.8%)	3,257,784; (12.5%)
	Caco2_INPUT_2	40,683,388	7,954,926; (19.6%)	5,717,731; (14.1%)
	Caco2_INPUT_3	33,214,425	6,393619; (19.2%)	3,729901; (11.2%)
	DLD1_CLIP	36,860,853	18,303,689; (49.7%)	10,826,660; (29.4%)
	DLD1_RNAseq	196,664,529	120,668,419; (61.4%)	111,056,779; (56.5%)
	Lovo_CLIP	35,860,144	16,426,136; (45.8%)	8,435,054; (23.5%)
	Lovo_RNAseq	193,142,724	130,200,660; (67.4%)	120,721,857; (62.5%)
Mouse	Colon_CLIP_1	62,821,728	18,841,261; (30.0%)	13,884,667; (22.1%)
	Colon_CLIP_2	63,087,357	22,749,788; (36.1%)	15,226,733; (24.1%)
	Colon_RNAseq_1	56,706,471	44,663,179; (78.8%)	34,097,906; (60.1%)
	Colon_RNAseq_2	62,437,020	51,525,926; (82.5%)	40,559,464; (65.0%)