mulinlab-pip

mulinlab bioinformatics pipelines for reproducible, efficient and convenient bioinformatics research.

Each pipeline is saved in a folder which is named by the pipeline name.

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Pre-processing

• MP_preSeq_FastQC: Quality control for NGS reads using FastQC

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DNA-seq

• MP_DNAseq_germline_GATK: Calling germline SNVs and InDels for single sample or cohort using GATK
• MP_DNAseq_common_CNV : Call copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments using R package ExomeDepth

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RNA-seq

• MP_RNAseq_RNACocktail: RNA-seq analysis using RNACocktail, from sequencing reads to differential expression genes, including several plots

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ChIP-seq

• MP_ChIPseq_BDS: Transcription Factor and Histone ChIP-seq processing pipeline using BDS (BigDataScript)

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ATAC-seq

• MP_ATACseq_BDS: ATAC-seq or DNase-seq data processing pipeline

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4C-seq

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• MP_4Cseq_4Cseqpipe: Mapping and analyzing 4C-seq experiments using 4Cseqpipe

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Hi-C

• MP_HiC_HiC-Pro: Hi-C data processing pipeline using HiC-Pro

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QTLs

• MP_eQTL_QTLtools: eQTL-mapping using QTLtools

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GWAS

• MP_GWAS: A suit of GWAS workflows for CHIMGEN project built on NEXTFLOW framework
• MP_GWAS_fine_mapping: Summary statistics based fine-mapping using three commonly-used tools