User story
As a biologist, I want to map R-loops using bisulfite-based approaches, so that I can get an accurate nucleotide-level map of R-loop locations.
Describe the solution you'd like
The current RSeq pipeline should be extended to allow for analysis of bisulfite-based seq data.
Known steps required
[ ] Research the pipeline/tools currently used for bisulfite-seq analysis (e.g., bismark)
[ ] Adjust the usage to allow for the new input modes
[ ] Adjust the process_input.R file to allow for the new input modes. The JSON config file generated by process_input.R should now indicate whether the sample is bisulfite-seq.
[ ] Adjust the snakemake pipeline to capture the bisulfite-seq configuration and store as a Boolean variable (e.g., is_bisulfite)
[ ] Create new rules for processing the bisulfite samples (i.e., when is_bisulfite is True)
[ ] Adjust the report template to account for bisulfite seq.
[ ] Update the quality models if appropriate
[ ] Conduct unit tests
[ ] Conduct user/sanity tests
[ ] Write relevant methods
Depends upon
May interact with quality models #4 #6 #5 but it not strictly dependent on them
User story As a biologist, I want to map R-loops using bisulfite-based approaches, so that I can get an accurate nucleotide-level map of R-loop locations.
Describe the solution you'd like The current RSeq pipeline should be extended to allow for analysis of bisulfite-based seq data.
Known steps required
is_bisulfite)is_bisulfiteisTrue)Depends upon May interact with quality models #4 #6 #5 but it not strictly dependent on them