Comments (2)
It should also optionally point to the IRmutations file. This is the only part of the pipeline which is actually specific at all to resistance, and just useful to our group as a quick look to see what mutations of interest are in the samples.
also
chromosome names?
snpEff - database name
overall dataset name?
from rna-seq-pop.
all complete bar, the option to trim. This will be added but not priority.
from rna-seq-pop.
Related Issues (20)
- add venn and heatmap to documentation HOT 1
- check codecov
- add tests for main functions in rnaseqpoptools
- In docs, do example analysis of bouake
- remove compkaryo and mpileup2readcounts submodules HOT 1
- rule that unzips a .fa.gz ref file HOT 1
- implement own gsea from GAF file
- move gwss into different folders based on window size HOT 1
- go on a code removal and tidying spree HOT 1
- Create Jupyter book and convert appropriate analyses to ipynb and papermill rather than py HOT 2
- Ensure meets FAIR principles and add to workflowhub.eu
- Configure conda envs so they work with conda channel priority = strict
- Allow .tsv or .xlsx or .csv metadata input HOT 1
- fix single-end reads with column input HOT 1
- xlsx and csv fail due to common.smk
- Change some config naming to make more sense HOT 1
- make isoform level DE optional
- provide singularity containers for the conda envs
- matplotlib can't import docstring causes error in checkinputs HOT 3
- remove venn diagrams HOT 1
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from rna-seq-pop.