eCLIP_Analysis

The repo contains list of all tools which were utilised in the Imig lab for analysis of eCLIP-seq data.

Preprocessing tools

1. Demultiplexing
2. Trimming and quality checks
3. Alignment
4. Peaks

Structure

1. Demux

• Script for demultiplexing files

2. Analysis_Pipeline

• Scripts for generating peaks from fastq file as input
• Requires STAR,samtools,bedtools,piranha,MEME,cutadapt

3. DEWSeq_Scripts

• Script to prepare input file for DEWSeq
• Run DEWSeq and generate plots
• Requires DEWSeq and htseq-clip