Description

PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP.

Input

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

meta2 (map)

Groovy Map containing reference information.
e.g. [ id:‘test’, single_end

]

ipbam (file)

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

controlbam (file)

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

ipbai (file)

BAM index

*.{bai}

controlbai (file)

BAM index

*.{bai}

input_control (boolean)

Whether to run PureCLIP with an input control

genome_fasta (file)

FASTA file of reference genome

*.{fa,fasta,fa.gz,fasta.gz}

Output

Name (Type)
Description
Pattern

meta (map)

Groovy Map containing sample information
e.g. [ id:'test', single_end:false ]

versions (file)

File containing software versions

versions.yml

Bed file of crosslinks

*.{bed}

peaks (file)

Bed file of peaks

*.{bed}
authors
Github user charlotteanne Github user marcjones
get in touch
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Tools

pureclip
GPL v3

PureCLIP is a tool to detect protein-RNA interaction footprints from single-nucleotide CLIP-seq data, such as iCLIP and eCLIP.

github.com/skrakau/PureCLIP pureclip.readthedocs.io/en/latest/GettingStarted https://github.com/skrakau/PureCLIP 10.1186/s13059-017-1364-2