Add results from B. altitudinis tests

[taylorreiter]

This pull requests integrates results and small changes from running the pangenome pipeline on B. altitudinis RNA seq samples.

The original idea for these samples was to see how well the pipeline worked when there was not a single good reference genome in our database for the organism that was sequenced. In the end, I realized that I didn't pick out a very good set of samples to explore this on; while initial results showed that these samples contained multiple strains/species, when I re-looked at these samples using abundance weighting, there was only one dominant species present. Nevertheless I want to integrate the analysis notebooks.

Files changed:

• gs_single_reference_genome.snakefile: updated to the new metadata file that contained the samples to be explored.
• pangenome_reference.snakefile: updated to the new metadata file that contained the samples to be explored. Also rearranged so that the sequences that are being used to build the transcriptome index are the ones that will be ortholog annotated using eggnog.
• scripts/utils.R: functions that will be used by a scripts/notebooks in this repo. The add an R2 and eq to a linear regression functions have been reviewed in other projects.
• notebooks/20220114_look_at_sra_org_composition.ipynb: adds a nb that looks at the composition of the publicly available isolate sequencing data
• notebooks/20220201_benchmark_salmon_vs_star_one_reference.ipynb: updates the regression code used for plots
• notebooks/20220215_benchmark_salmon_vs_star_no_best_reference.ipynb: looks at the results of running these snakefiles on the B. alt samples
• notebooks/20220217_summarize_rnaseq_sourmash_gather_results.ipynb: looks at gather results, comparing abundance-weighted to non abudance weighted taxonomy composition of the samples

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[taylorreiter]

Oh that's really cool! Do you have a repo or a paper describing the project? I would love to see it if you do!

[ben-heil]

Oh that's really cool! Do you have a repo or a paper describing the project? I would love to see it if you do!

I don't think it ever worked well enough to become a full package unfortunately :(