Comments (3)
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)
from rna-seq-pop.
Given coluzzii and gambiae will both use PEST, for now, its probably acceptable to run separate species in separate snakemake directories
from rna-seq-pop.
closing as the above workaround is reasonable
from rna-seq-pop.
Related Issues (20)
- allowing custom snpEff databases HOT 4
- Change 'chrom' to 'contig' HOT 1
- add CIs to Variants of interest module HOT 1
- change freebayes min depth param HOT 2
- Problem installing the rna-seq-pop HOT 6
- Implement Anopheles gambiae AIMs chromosome plot
- Change syntax for contrasts
- Implement venn diagrams of expressed genes HOT 1
- Make video tutorial/walkthrough HOT 2
- Implement heatmap script
- implement single-end read functionality HOT 1
- add venn and heatmap to documentation HOT 1
- check codecov
- add tests for main functions in rnaseqpoptools
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- remove compkaryo and mpileup2readcounts submodules HOT 1
- rule that unzips a .fa.gz ref file HOT 1
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