https://github.com/bartongroup/differr_nanopore_DRS

Scripts for identifying sites with differential error rates in mapped nanopore DRS data
https://github.com/bartongroup/differr_nanopore_DRS

Last synced: 2 months ago
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Scripts for identifying sites with differential error rates in mapped nanopore DRS data

• Host: GitHub
• URL: https://github.com/bartongroup/differr_nanopore_DRS
• Owner: bartongroup
• Created: 2019-02-04T12:42:25.000Z (almost 6 years ago)
• Default Branch: master
• Last Pushed: 2020-11-27T09:29:12.000Z (about 4 years ago)
• Last Synced: 2024-08-03T23:18:22.620Z (5 months ago)
• Language: Python
• Homepage:
• Size: 15.6 KB
• Stars: 10
• Watchers: 3
• Forks: 3
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

Awesome Lists containing this project

• awesome-nanopore - DiffErr - [Python] - A tool for detecting modifications from Nanopore DRS errors using a low modification control. (Software packages / RNA modification analysis)

README

        
## A tool for detecting modifications from Nanopore DRS errors using a low modification control

### How to use:

* Basecall & map direct RNA data (all datasets **MUST** be sequenced at approximately the same time with the exactly the same flowcell/kit/MinKNOW software, and basecalled and mapped in the same way with the same model, otherwise you **WILL** get loads of false positives. Nanopore update their pores/kits/models/software all the time, so be wary...).

* Run `differr` on mapped bam files.

* Output from `differr` is a bed file with the positions with significantly altered error, and a optional hdf5 file with all of the per reference base basecalls, which might be useful for further analyses.

* Columns of bed file are:

    * chrom, start, end, name

    * score: -log10 of the FDR, rounded to nearest whole number

    * strand

    * odds ratio: the change in the ratio of matches to mismatches in the wild type compared to the mutant with low modifications. An odds ratio > 0 indicates more modifications in the WT.

    * G statistic for the comparison of pooled WT and mutant samples.

    * -log10 P value for the comparison of pooled WT and mutant samples.

    * -log10 FDR for the comparison of pooled WT and mutant samples.

    * G statistic for the homogeneity test of mutant replicates.

    * -log10 P value for the homogeneity test of mutant replicates.

    * G statistic for the homogeneity test of wild type replicates.

    * -log10 P value for the homogeneity test of wild type replicates.