tdido / board_alegosto01 Goto Github PK

The idea would be to create a GitHub repository to host the tutorial code, to use it also as practice of GitHub usage. We would then create a new repository for the project itself.

https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html

Try to follow it and we can discuss any questions.

https://bioinfo-lessons.gitlab.io/intro-git/

generate bam with minimap file that it's going to be used by nanopolish.

• Multiple Myeloma Guide
• A decade of structural variants: description, history and methods to detect structural variation
• Structural variant calling: the long and the short of it
• Revealing the Impact of Structural Variants in Multiple Myeloma

Conda is a package manager which, through the "bioconda" channel, gives you access to tons of bioinformatics tools. You can check the bioconda channel's docs to set it up and read a bit more about it.

You can set it up both in your machine and in the cluster.

NOTE: instead of using the miniconda installer as linked in the bioconda docs, I suggest using mambaforge instead.

• Set up cluster user
• Read docs
• Check SSH access
• General intro to cluster architecture (compute, storage)
• Try Screen for persistent terms

You have instructions for using slurm to submit commands to the queues in the cluster docs, but let's use this issue in case you have some questions that we could leave documented for future reference.

This will be the first step of the pipeline.

Implement the following software into a Snakemake pipeline to QC nanopore data

• https://github.com/wdecoster/NanoPlot
• https://github.com/GenomiqueENS/toulligQC
• https://github.com/a-slide/pycoQC

We will then look at the output and decide whether to keep one or more of them.

Data is located at /storage/scratch01/groups/bu/myeloma_altum