SeqPlots R workflow

Przemyslaw Setmpor

Abstract

SeqPlots is a tool for plotting average track signals (e.g. read coverage) and sequence motif densities over user specified genomic features. The data can be visualized in linear plots with error estimates or as series of heatmaps that can be sorted and clustered. The software can be run locally on a desktop or deployed on a server and allows easy data sharing. SeqPlots pre-calculates and stores binary result matrices, allowing rapid plot generation. Plots can also be run in batch.

Package

SeqPlots 1.16.0

Contents

1 Quick start demo

1. Start SeqPlots. Refer to installation guides for platform specific information. After successful initiation the web interface should automatically open in your default web browser. If you are using web server version just navigate your browser to the server address.

   

   The SeqPlots interface in web browser

2. Upload feature (BED or GFF) and track (BigWig or WIG) files. They can be gzip compressed (e.g. file1.bed.gz). Press green “Add files…” button or just drag and drop files into the window. The ready to upload files will show up in upload window, where you select user name, reference genome and optionally add some comments.

   

   File upload panel

3. When all is done press blue “Start upload” button. After upload and processing is done the green “SUCCESS” label should show. It means that file is on the registered and ready to use. Occasionally the file might be mot formatted properly or chromosome names might not agree with reference genome. In such case a verbose error will window appears and file as labeled as “ERROR”. For further information please refer to errors chapter.