{"repo":"nf-core/clipseq","free":true,"listed":false,"github":"https://github.com/nf-core/clipseq","clone":"git clone https://github.com/nf-core/clipseq.git","description":"CLIP sequencing analysis pipeline for QC, pre-mapping, genome mapping, UMI deduplication, and multiple peak-calling options.","language":"Nextflow","stars":25,"topics":["workflow","pipeline","nextflow","clip","nf-core","peak-calling","clip-seq","rna-rbp-interactions"],"license":"MIT","category":"workflow-automation","readme_excerpt":"Introduction nf-core/clipseq is a bioinformatics best-practice analysis pipeline for CLIP (cross-linking and immunoprecipitation) sequencing data analysis to study RNA-protein interactions. The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. Pipeline Summary By default, the pipeline currently performs the following: 1. Adapter and quality trimming ( Cutadapt ) 2. Pre-mapping to e.g. rRNA and tRNA sequences ( Bowtie 2 ) 3. Genome mapping ( STAR ) 4. UMI-based deduplication ( UMI-tools ) 5. Crosslink identification ( BEDTools ) 6. Bedgraph coverage track generation ( BEDTools ) 7. Peak calling (multiple options): - iCount - Paraclu - PureCLIP - Piranha 8. Motif detection ( DREME ) 9. Quality control: - Sequencing quality control ( FastQC ) - Library complexity ( Preseq ) - Regional distribution ( RSeQC ) 10. Overall pipeline run and QC summaries and peak calling comparisons ( MultiQC ) Quick Start 1. Install nextflow 2. Install any of Docker , Singularity , Podman , Shifter or Charliecloud for full pipeline reproducibility (please only use Conda as a last resort; see docs) 3. Download the pipeline and test it on a minimal dataset with a single command: Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile i","default_branch":null,"files":null,"tree":[],"storefront":"/r/nf-core","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/nf-core/clipseq/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}