EVOLINC-I: A rapid Long-Intergenic Noncoding RNA (lincRNA) detection pipeline

Introduction

Evolinc-I is a long intergenic noncoding RNA (lincRNA) identification workflow that also facilitates genome browser visualization of identified lincRNAs and downstream differential gene expression analysis.

Evolinc-I minimally requires the following input data

1. A set of assembled and merged transcripts from Cuffmerge or Cuffcompare in gene transfer format (GTF)
2. A reference genome (FASTA)
3. A reference genome annotation (GFF/GTF/GFF3)

Optional input data

1. Transposable Elements database (FASTA)
2. Known LincRNA (GFF)
3. Transcription start site coordinates (BED)

Availablility

Using Docker image

Since there are several dependencies (these can be seen in Dockerfile) for running Evolinc-I on your linux or MAC OS, we highly recommend using the available Docker image for Evolinc-I or the Dockerfile to build an image and then use the built image. Docker can be installed on any of three platform using the instructions from Docker website. You can also try Play-With-Docker for running Evolinc-I using the below instructions

# Pull the image from CyVerse Dockerhub
docker pull evolinc/evolinc-i:1.7.5

# See the command line help for the Docker image
docker run evolinc/evolinc-i:1.7.5 -h 

# Download some sample data 
git clone https://github.com/Evolinc/Evolinc-I.git
cd Evolinc-I/sample_data

# Run Evolinc-I With mandatory files
docker run --rm -v $(pwd):/working-dir -w /working-dir evolinc/evolinc-i:1.7.5 -c Sample_cuffcompare_out.gtf -g TAIR10_chr1.fasta -u TAIR10_chr1_genes.gff -o test_out -n 4

# Run Evolinc-I With both mandatory and optional files
docker run --rm -v $(pwd):/working-dir -w /working-dir evolinc/evolinc-i:1.7.5 -c Sample_cuffcompare_out.gtf -g TAIR10_chr1.fasta -u TAIR10_chr1_genes.gff -b TE_RNA_transcripts.fa -t Sample_TSS_data.gff -x Sample_known_lncRNAs.gff -o test_out -n 4

Using CyVerse Discovery Environment

The Evolinc-I app (search Evolinc-I in the search box of the apps window) is currently integrated in CyVerse’s Discovery Environment (DE) and is free to use by researchers. The complete tutorial is available at this CyVerse wiki. CyVerse's DE is a free and easy to use GUI that simplifies many aspects of running bioinformatics analyses. If you do not currently have access to a high performance computing cluster, consider taking advantange of the DE.

Step-by-step walkthroughs

Step-by-step walkthrough for running Evolinc-I on DE is available here. Step-by-step walkthrough for the command-line, with directions on how to change parameters is coming soon. Information on how to easily create a Cuffmerge/Cuffcompare input file from 1-many SRA IDs within the DE can be found here

Issues

If you experience any issues with running Evolinc-I (DE app or source code or Docker image), please open an issue on this github repo. Alternatively post your query or future requests in this google group

Copyright free

The sources in this Github repository, are copyright free. Thus you are allowed to use these sources in which ever way you like. Here is the full MIT license.

Citing Evolinc-I

If you have used Evolinc-I manuscript in your research, please cite as below..

Andrew D. Nelson*, Upendra K. Devisetty*, Kyle Palos, Asher K. Haug-Baltzell, Eric Lyons, Mark A. Beilstein (2017). "Evolinc: a comparative transcriptomics and genomics pipeline for quickly identifying sequence conserved lincRNAs for functional analysis". Frontiers in Genetics. 1(10)