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README.md
Singularity

README.md

  • Do you want to learn how to align RNA-sequences to a reference genome?

  • Do you want to bypass the process of installing alignment software and get a preview into a panel of different alignment strategies?

  • Do you want to compare how popular mapping algorithms perform on your data?

Then this is the tutorial for you! Please proceed to our wiki

Just interested in comparing two or more .bam files? Check out bamdiff

Docker

A Docker image is available for this project. For a detailed description of docker, please refer to this overview.

Install Docker

Follow instructions to install Docker for your environment.

Get a pre-built image from DockerHub and run the server
docker pull stevetsa/rna_mapping
docker run -it stevetsa/rna_mapping

At the root prompt inside the container, execute the script - 
/RNA_mapping/build/doAll.sh

Singularity

Run this image on the NIH biowulf cluster

sinteractive --cpus-per-task=16 --mem=10g
module load singularity
singularity shell docker://stevetsa/rna_mapping
 
inside Singularity container, execute the script - 
/RNA_mapping/build/doAll.sh