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sanjaynagi / rna-seq-pop

Snakemake workflow for Illumina RNA-sequencing experiments - extract population genomic signals from RNA-Seq data
https://sanjaynagi.github.io/rna-seq-pop/
MIT License
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Decide what to do if multiple species regarding reference genomes #7

Closed sanjaynagi closed 3 years ago

sanjaynagi commented 3 years ago

Should we allow separate species to be run in one go? also of extra importance as coluzzii and arabiensis genomes are improved (Zamyatin et al, 2020)

sanjaynagi commented 3 years ago

one possibility is a dataframe which contains the species and links to to the various reference files. this would at least be easily accessible within R.

otherwise, not sure how would be best to dispatch an RScript for each species separately. one could use wildcards, and then determine the reference input based on the wildcards. that is an option. There is no real reason why we need to run a single script for all species, we are not particularly interested in, for example, a PCA of all the species (maybe we are)

sanjaynagi commented 3 years ago

Given coluzzii and gambiae will both use PEST, for now, its probably acceptable to run separate species in separate snakemake directories

sanjaynagi commented 3 years ago

closing as the above workaround is reasonable