Today - we used our SraExplorer to subset the data we were interested. It is a short class, so we wanted a small dataset:
Targeted human RNASequencing data
You will find 3 different data sets, which we will use to run the RNA-sequencing Nextflow workflow we forked from the community-based standard group nf-core.
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First we searched with the terms targeted[All Fields] AND ("Homo sapiens"[Organism] OR human[All Fields]) in Sra-explorer
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Then we selected a project and we searched with this term PRJNA564604[All Fields] also in Sra-explorer
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Then we selected all the samples, clicked on the Full Metadata tab and downloaded these files to our laptop and uploaded them to Zenodo shown in the gif here
The metadata file was edited using emacs - an editor available on most systems, to limit the full metadata list to just the accessions
Today we are running a forked version of the nf-core RNASeq nextflow workflow. Nextflow has a lot of nice features when you are running, these options for everything from generating timing of execution, traces, to creating a directed-acyclic-graph (DAG). You can find the documentation here. I would check it out and have some fun exploring these options.
For us, our
[forked RNA-seq DAG]
