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Figure 1 | Genome Biology

Figure 1

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

Figure 1

PIPE-CLIP overview. (A) Flowchart of PIPE-CLIP. Mapping results (in SAM/BAM format) are first filtered, and users then have an option to remove PCR duplicates. The filtered mapping files are then used to identify enriched clusters and reliable mutations. Each enriched cluster with at least one reliable mutation is then reported as a cross-linking region. (B) A screenshot of the PIPE-CLIP website. Users can upload SAM/BAM input files and perform customized data analysis by adjusting different parameters. Default parameters are provided based on our empirical experience. All of the parameters are automatically documented, so that the analysis procedure and results can be easily reproduced. A tool for removing PCR duplicates of iCLIP raw fastq data, according to specific barcodes, is also provided. (C) A sample output figure generated by running PIPE-CLIP reporting the length distribution of the mapped reads. (D) A demonstration of the output table for candidate cross-linking regions. The annotation of each column is detailed in the online user manual.

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