Implement Hidden-Markow-Models implemented in ChromstaR for genome-wide characterization of open chromatin landscape
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Description
Hi everybody,
a nice feature would be to additionally have Hidden-Markow-Models as implemented in ChromstaR for genome-wide characterization of open chromatin landscape. The approach would be as described here: "On this approach control and stress condition were processed in two steps: (1) we fitted a univariate HMM over each ATAC-seq samples individually and (2) we performed a multivariate HMM over the combined ATAC-seq samples in each condition. For that, BAM files were processed under the differential mode, with a false discovery rate (FDR) cutoff of 0.05 and bin size of 500" Source: http://dx.doi.org/10.1101/824789
Again, thank you for your time!
Cheers
Temperche
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Research direction
No files, tests, or entry points are identified in the issue. Start by reviewing the cited ChromstaR approach and determine where this pipeline could support univariate and multivariate HMM processing; done means the requested analyses are integrated with the stated FDR cutoff and 500 bp bin size.
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Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100