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 ]

ipbam

:file

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

controlbam

:file

Sorted BAM/CRAM/SAM file

*.{bam,cram,sam}

meta2

:map

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

ipbai

:file

BAM index

*.{bai}

controlbai

:file

BAM index

*.{bai}

meta3

:map

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

genome_fasta

:file

FASTA file of reference genome

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

input_control

:boolean

Whether to run PureCLIP with an input control

Output

name:type
description
pattern

crosslinks

meta

:map

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

${crosslinks_output_name}

:file

Bed file of crosslinks

*.{bed}

peaks

meta

:map

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

${peaks_output_name}

:file

Bed file of peaks

*.{bed}

versions

versions.yml

:file

File containing software versions

versions.yml

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
maintainers
Github user charlotteanne
Github user marcjones
get in touch
Ask a question on Slack Open an issue on GitHub