https://github.com/mikelove/swimdown
Code for generating and evaluating the simulation for "Swimming Downstream"
https://github.com/mikelove/swimdown
Last synced: 3 months ago
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Code for generating and evaluating the simulation for "Swimming Downstream"
- Host: GitHub
- URL: https://github.com/mikelove/swimdown
- Owner: mikelove
- Created: 2018-06-18T13:31:43.000Z (almost 7 years ago)
- Default Branch: master
- Last Pushed: 2022-03-08T15:57:57.000Z (about 3 years ago)
- Last Synced: 2025-01-22T07:51:19.139Z (4 months ago)
- Language: HTML
- Size: 21.3 MB
- Stars: 6
- Watchers: 2
- Forks: 3
- Open Issues: 0
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Metadata Files:
- Readme: README.md
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README
# "Swimming downstream" evaluation code
This repository contains all the code used in the evaluation of
methods for DTU, DGE, and DTE in the F1000Research article,
*Swimming downstream: statistical analysis of differential transcript*
*usage following Salmon quantification*. The directories contain the
following analyses:
* `countsimqc` - generate the countsimQC report (and the report)
* `dte` - generate the DGE and DTE evaluations
* `dtu` - generate the DTU evaluation
* `quant` - bash scripts to quantify the abundances
* `rats` - run RATs
* `simulate` - generate the simulated reads
* `suppa` - run SUPPA2
Note on the code in `simulate`: simulating reads proceeds in three
steps: 1) `simulate_expression.R` is used to simulate expression
vectors for two groups with DGE, DTE, and DTU genes, 2)
`simulate_reads.R` is used to actually simulate the paired-end reads
with the *polyester* package, 3) `shuffle_wrapper.sh` is used to
shuffle and then compress the paired-end reads output by
*polyester*. The simulated reads need to be shuffled to be input to
*Salmon* (because *polyester* outputs reads from each transcript, one
at a time).
*DRIMSeq* and *DEXSeq* were run using the code directly from the
`rnaseqDTU` workflow, see .