Basic usage of PARANOiD

Description of the minimal setup required for running PARANOiD.

The minimal setup includes: FASTQ file containing reads, a reference genome and a barcode file. Generated outputs include alignments, cross-link sites in three different file formats, an overview of the peak height distribution, :ref:` processing statistics <output-statistics>`, strand distributions and an IGV session file which can be loaded directly into the IGV to visualize first results. A directory named output (unless stated otherwise) containing all results will be generated. All parts marked with <> are files that need to be specified by the user.

nextflow /path/to/directory/PARANOiD.nf --reads <read-file> --reference <reference-file> --barcodes <barcode-file>