pisces
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Novartis
PISCES is a pipeline for rapid transcript quantitation, genetic fingerprinting, and quality control assessment of RNAseq libraries using Salmon.
- [ ] add "housekeeping genes" parameter to config.json - [ ] add code to build "housekeeping" salmon index files for determining sample type - [ ] add code to...
There are empty output tables that are written for backward compatibility with older versions of pisces. I should add a warning to explain the the tables are empty, and recommend...
From the GTF file we will need to capture the gene description annotation.
I accidentally removed the tidy data format from my last update. This time I will add a `--tidy` flag for `pisces summarize-expression` that will change outputs to tall/tidy shape.
It's not clear if DESeq2 is the best choice for DTE, or if we should use salmon's inferential replicates and run swish instead. If the latter, then it makes sense...
- [ ] Library geometry from salmon - [ ] FLD from salmon - [ ] Position specific bias model information - [ ] Ribosomal RNA percent
Path to Salmon binary is now hardcoded. It would be better when PISCES would check if salmon is in the PATH eg. like here https://stackoverflow.com/questions/377017/test-if-executable-exists-in-python.
- [x] Add a Dockerfile to define build process and entry point - [ ] Set up gh-actions to build docker images and publish to Docker hub