| PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP. It accepts mapped eCLIP/iCLIP reads in BAM format as input and also supports control library and crosslink-associated (CL) motifs input for bias correction. PureCLIP outputs two BED files, containing the found crosslink sites (first file) and binding regions (second file) that merge nearby crosslink sites to contiguous regions (region width controlled by -dm parameter). By default, the tool parameters are set to values optimized for proteins binding to short defined binding regions, e.g. proteins binding to short specific motifs such as PUM2 and RBFOX2. This behaviour can be changed with the -bc option. The default setting -bc 0 is equivalent to manually setting -bdwn 50 -ntp 10 -ntp2 0 -b1p 0.01 -b2p 0.15. The second setting -bc 1 is designed for RBPs that produce larger clusters (proteins causing larger crosslink clusters with relatively lower read start counts, e.g. proteins binding to low complexity motifs). -bc 1 corresponds to the manual setting -bdwn 100 -antp -b2p 0.01 -b2p 0.1. |
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/pureclip
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| - HMM based peak caller designed for eCLIP/iCLIP data | 1.0.4 | 16.01 | |