board_alegosto01's People
board_alegosto01's Issues
fast5 to fastq (poortools)
Snakemake tutorial
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
Git tutorial
Try to follow it and we can discuss any questions.
minimap-samtools-nanopolish
generate bam with minimap file that it's going to be used by nanopolish.
Introductory reading material
Conda setup
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.
workflow directory organization
Cluster access
- Set up cluster user
- Read docs
- Check SSH access
- General intro to cluster architecture (compute, storage)
- Try Screen for persistent terms
qualcosa da aggiungere
.gitignore configuration
resources function in snakefile
Slurm usage
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.
QC data
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
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