PET: a Pipeline for Enhancer Transcription, a tool for quantify active enhancer RNAs from RNA-seq data
The aim of this project is to quantify transcribed enhancers with a simple command. We will keep on updating it.
Bpipe, fastp, STAR, FeatureCounts
conda install -c bioconda bpipe
conda install -c bioconda fastp
conda install -c bioconda star
conda install -c bioconda subread
git clone https://github.com/fun-science-club-ntu/PET
bpipe pipeline.txt rnaseq_1.fastq.gz rnaseq_2.fastq.gz
Index directory of STAR can be changed at the first line pipeline.txt.
This pipeline now supports the Homo sapiens (hg19).
Fastq files
Enhancer RNA counts matrix will be in ./count/rnaseq.tab
Quality control and trimmed FASTQ file will be in ./trim/rnaseq.fastq.gz
Aligned BAM file will be in ./mapped/rnaseq.bam
We recommand GREAT (http://great.stanford.edu/public/html/) for functional enrichment analysis and Deseq2 (https://bioconductor.org/packages/release/bioc/html/DESeq2.html) for differential expression analysis.
Yingcheng Wu, et al. Multi-omics analysis reveals the functional transcription and potential translation of enhancers. International journal of cancer. vol. 147,8 (2020): 2210-2224. doi:10.1002/ijc.33132
PI: Yihui Fan, MD, PhD
Jiangsu Distinguished Professor
Director and Professor, Department of Pathogenic Biology, School of Medicine, Nantong University, Nantong, Jiangsu, China.
Any technical question please contact [email protected] (Yingcheng Wu)
Copyright (C) 2019-2021 Fan Lab @ NTU.