TODO

1. nasal_mrna_7s: {species}_{hisat/salmon}__{celltype}_{libtype}_{condition}_{table/sig}_{date}
2. sva plot in xlsx, add check for failure
3. upload cpm tables in separate directory – inside excel I think
4. create a factor of {detection}_{libtype} so that we have 4 colors to view the clustering of all samples together.
5. Create separate blocks for the different library types to make the worksheet easier to step through.
6. Explicit kraken2 of nasal and skin samples – potentially use kmcp.

1. 7SL positive vs negative for
2. Add plot of transcriptome clustering of nasal swabs between nasal positive/negative with the caveat that the are only 2 positives, 8 negatives, and 1 undetermined in the stranded library; the ribozero have 5 positive, 3 negative, and 1 undetermined.
3. Create a relative abundance of bacteria/viruses observed in the nassal samples; counting at genus.

Note that this requires splitting the data into 4 groups: salmon+rz, salmon+mrna, hisat+rz, hisat+mrna.

1. We have some samples which are defined as persistent via 7SL. Can we see some reads in those samples?
2. Send file with mapped reads per sample for all human samples.
3. Queue SL read counter for all human samples.
4. All samples have nasal, skin, PBMC; all patients are nasal + or nasal -; perform contrasts of nasal+/nasal- of the PBMC samples. For the PBMC samples, recast them as +/-

1. We have some samples which are defined as persistent via 7SL. Can we see some reads in those samples?
2. Send file with mapped reads per sample for all human samples.
3. Queue SL read counter for all human samples.
4. All samples have nasal, skin, PBMC; all patients are nasal + or nasal -; perform contrasts of nasal+/nasal- of the PBMC samples. For the PBMC samples, recast them as +/-