![]() This has often already been done as part of demultiplexing an Illumina sequencing run. Optionally, UMI-tools is used to extract the UMI from the beginning of the read and append it to the read name using _ as a delimiter. They may contain adapter sequence and potentially regions with low quality. NB: The FastQC plots displayed in the MultiQC report shows untrimmed reads. *_fastqc.zip: Zip archive containing the FastQC report, tab-delimited data file and plot images.*_fastqc.html: FastQC report containing quality metrics for your untrimmed raw fastq files.It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences.įor further reading and documentation see the FastQC help pages. MultiQC - CLIP summary metrics and QC for raw reads, alignment, PCR deduplication, library complexity and crosslink distribution over genomic featuresįastQC gives general quality metrics about your sequenced reads.RSeQC - Crosslink distribution over genomic features.BEDTools - Single-nucleotide crosslink position identification.UMI-tools - UMI-based PCR deduplication.Bowtie 2 - Pre-alignment to rRNA and tRNA sequences. ![]() Cutadapt - Adapter and quality trimming.UMI-tools - Extract UMI from FastQ read and append to read name.The pipeline is built using Nextflow and processes data using the steps described in the main README.md. All paths are relative to the top-level results directory. The directories listed below will be created in the results directory after the pipeline has finished. The plots are taken from the MultiQC report, which summarises results at the end of the pipeline and also includes CLIP-specific summary metrics. This document describes the output produced by the pipeline.
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