Use the following workflows for an automatized data analysis for iCLIP and eCLIP data. (G-I) Example output of RCAS (RNA Centric Annotation System) (G) showing the binding coverage for the transcript and the 5’ and 3’ UTR, (H) depicting the binding coverage around the exon-intron boundaries, (I) and a generated target distribution plot which states what kind of RNAs the protein of interest prevalently binds to. (F) Sequence motifs of MEME-Chip (DREME and MEME) from binding sequence motifs that were predicted from potential binding regions (peaks) obtained by a peak caller like PEAKachu, Piranha or PureCLIP. (E) Output of FastQC showing the duplication levels of the read libraries. (D) Output of CollectInsertSizeMetrics estimating the insert size for the read libraries. (C) Output of plotFingerprint that shows the read coverage for the CLIP-Seq and control samples. (A) Galaxy CLIP-Explorer workflows and tools (B) Output of multiBamSummary and plotCorrelation comparing two biological replicates of a CLIP-Seq experiment and one control sample. Galaxy CLIP-Explorer – Many Possibilities CLIP-Explorer can handle multiplexed and de-multiplexed eCLIP and iCLIP data in FASTQ and FASTA format. We processed eCLIP data with around 20 million reads from Nostrand et al.
Galaxy CLIP-Explorer can process large CLIP-Seq data of eCLIP and iCLIP. The Galaxy Training Network tutorial uses eCLIP data from human liver cancer cells (Hep G2) and is hosted on zenodo: We recommend to follow the tutorial on FastQC for quality checks and the tutorial for IGV for data inspection. The underlying workflow of the tutorial can be found here. The tutorial will help you to understand the analysis steps and the most important parameters and tools that are used in CLIP-Explorer. You have CLIP-Seq data, but you need some guidance for the CLIP-Seq data anlysis? Take a look at the CLIP-Seq data analysis tutorial on the Galaxy Training Network where you can analyse CLIP-Seq data of RBFOX2 from human liver cancer cells (Hep G2). Getting Started with Galaxy CLIP-ExplorerĪre you new to Galaxy? Are your returning after a long time, and looking for help to get started? Then take a guided tour through the user interface of Galaxy. Welcome to the Galaxy CLIP-Explorer – a webserver to process, analyse and visualise CLIP-Seq data.ġ.
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