ugrbioinfo/methylextract2 repository overview

⁠MethylExtract2

⁠1. Get started: Load methylExtract2 docker container

FIRST USE

First time you load our docker container you will need to follow the next steps:

docker push ugrbioinfo/methylextract2:latest

Then you can run the docker container

docker run --hostname methylExtract2 --name methylExtract2 -it methylextract2:latest

SUBSEQUENT USES

After first use you can stop the methylExtract2 container with the following:

docker stop methylExtract2

And for further uses you’ll have to use the following to start the container:

docker start methylExtract2

docker exec -it methylExtract2 /bin/bash

⁠2. Get and prepare an assembly and the config file

The software prepareAssembly download all files of an assembly and prepares it for methylExtract use and it also write a config file for this assembly. It works with all UCSC available assemblies and with custom assembly files.

Example of use:

prepareAssembly --ucsc hg38 --label hg38 --threads 2 --library PE

This command will download hg38 assembly and it will create a config file in /home/methylextract/config.txt (as default) for a paired-end sequencing data and 2 threads.

⁠3. Configuration file explanation

MethylExtract2 needs a config file that it’s created by prepareAssembly software and by default placed in /home/methylextract/config.txt.

⁠4. Methylation profiling

⁠a. SRA sample

MethylExtract2 --input _SRX/SRR_ --config _configFile_ --outdir _outDir_

⁠Example of an SRX profiling:

MethylExtract2 --input SRX1631736 --config /home/methylextract/config.txt --outdir /home/methylextract/outputMethylomesSRX

⁠Example of an SRR profiling:

MethylExtract2 --input SRR3225632 --config /home/methylextract/config.txt --outdir /home/methylextract/outputMethylomesSRR

⁠b. Custom input

MethylExtract2 --input Examples --config /home/methylextract/config.txt --outdir /home/methylextract/outputMethylomesCustom