lsbnb/galaxy_atacgraph repository overview

⁠This image is provided by Institute of Plant and Microbial Biology and Institute of Information Science, Academia Sinica.

⁠Contact information:

⁠Pao-Yang Chen ([email protected]⁠); LAB website:https://paoyang.ipmb.sinica.edu.tw⁠

⁠Chung-Yen Lin ([email protected]⁠); LAB website: http://eln.iis.sinica.edu.tw⁠

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⁠Description

It is a galaxy docker designed for ATACgraph. ATACgraph is a simple and effective software for the analysis of ATAC-Seq data. It contains 12 analyses to profile (epi)genome.

⁠ATACgraph modules：https://github.com/RitataLU/ATACgraph⁠

⁠00_rmChr : Remove chrM,chrPt

⁠00_blacklist : Remove blacklist overlapped regions

⁠01_calFragDist : Generate figures of fragments size distribution & Fast Fourier transform

⁠02_selectFragSize : Select bam fragments size

⁠02_gtftoBed : Transform gtf file to bed files

⁠03_callPeak : Call ATAC-seq peaks

⁠03_genePlot : Generate figures of depicting genes and peaks accessibility

⁠03_junctionBed : Generate junction bed track

⁠04_specificPeaks : Identify specific peaks between 2 groups of peaks

⁠04_specificPeaksIDR : Identify specific peaks with Irreproducibility Discovery Rate (IDR) framework

⁠04_specificPromoter : Identify specific promoter using Gaussian Mixture Model between 2 groups of peaks

⁠05_seqCompare : Compare peaks between ATAC-seq and Other seq

⁠05_compareToRNA : Comparison of accessible genes and genes expression

⁠Workflow

⁠1.Filtering reads overlapping with blacklist regions

⁠2.Filtering chromosome and generating figures of fragment distribution and Fast Fourier analysis

⁠3.Filtering reads chromosome and creating junction files for IGV visualization

⁠4.Defining the differential peaks with specific fragments size

⁠5. Integrating ATAC-seq with other NGS data

⁠6.Integrating ATAC-seq with RNA-seq

⁠7.Visualizing the chromatin accessibility and the fold enrichment of open regions in genomic features

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⁠Install & Usage

⁠Step 1. docker pull lsbnb/galaxy_atacgraph

⁠Step 2. mkdir galaxy_guest

⁠Step 3. docker run -d -t -i -p 8081:80 -p 8021:21 -p 8022:22 -v $('pwd')/galaxy_guest/:/root/galaxy/database/ftp/[email protected]/ lsbnb/galaxy_atacgraph /bin/bash

⁠Step 4. Start with your analysis, if you are new to Galaxy --> Please start your jouourney from https://galaxyproject.org/learn/⁠

⁠Step 5. Open your browser and type your host IP address, ex. http://your.host.IP.address:8081/⁠

⁠Step 6. login as [email protected]⁠ with password rnaanalysis. And please take the section about "how to upload data" to import the data for galaxy.

⁠Step 7. Select ATACgraph from left panel and choose any module you want to use.

⁠Step 8. Or select the workflow from left panel, get the result more quickly and efficiently.

⁠How to upload files

A. If the size of file is less than 2GB, please use "ATACgraph --> upload file --> choose local file".

B. For those files > 2GB, two approaches below you can choose.

B1. Use "ATACgraph --> upload file --> paste and fetch data" to paste the URLs to get the files. ex. ftp:

B2. Use "ATACgraph --> upload file --> choose FTP file". In our script for starting the docker (lsbnb/galaxy_atacgraph), we have mounted the local directory named as "galaxy_guest" at localhost. So you can find the directory in the home directory you executed the DOCKER image. Please copy or ftp those files for analysis in this directory, then you can find them when you click the button "choose FTP site".