PIPE-CLIP: a comprehensive online tool for CLIP-seq data analysis

Table 3 Cross-linking regions identified by PIPE-CLIP for the Ago HITS-CLIP data

	FDR <0.1	FDR <0.05	FDR <0.01	FDR <0.001	FDR <0.0001
Enriched clusters	58,614	41,390	20,781	8,744	6,288
Reliable mutations	14,957	14,271	5,872	5,546	5,044
Cross-linking regions	3,778	2,833	1,232	534	328

The total numbers of cross-linking regions identified by PIPE-CLIP using different FDR thresholds are shown. The FDR thresholds are the same for both the procedure of looking for enriched clusters and reliable mutations.

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