https://github.com/xueyidong/longreadbenchmark
Benchmarking long-read RNA-seq analysis tools
https://github.com/xueyidong/longreadbenchmark
Last synced: 5 months ago
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Benchmarking long-read RNA-seq analysis tools
- Host: GitHub
- URL: https://github.com/xueyidong/longreadbenchmark
- Owner: XueyiDong
- License: mit
- Created: 2021-04-26T07:53:09.000Z (almost 4 years ago)
- Default Branch: master
- Last Pushed: 2024-01-30T01:54:45.000Z (about 1 year ago)
- Last Synced: 2024-11-09T19:39:51.887Z (5 months ago)
- Language: R
- Size: 9.83 MB
- Stars: 25
- Watchers: 2
- Forks: 2
- Open Issues: 1
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Benchmarking long-read RNA-sequencing analysis tools using in *in silico* mixtures
This repository contains the code used to perform the analysis and generate the figures in this paper:
**Benchmarking long-read RNA-sequencing analysis tools using in silico mixtures**
Xueyi Dong, Mei R. M. Du, Quentin Gouil, Luyi Tian, Jafar S. Jabbari, Rory Bowden, Pedro L. Baldoni, Yunshun Chen, Gordon K. Smyth, Shanika L. Amarasinghe, Charity W. Law, Matthew E. Ritchie
Nature Methods 2023; doi: [https://doi.org/10.1038/s41592-023-02026-3](https://doi.org/10.1038/s41592-023-02026-3)
## Data Availability
Our RNA-seq data are available from Gene Expression Omnibus (GEO) under accession number [GSE172421](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE172421) (main benchmarking dataset) and [GSE227000](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE227000) (lab-based mixture of replicate 1).
Please cite [our paper](https://doi.org/10.1038/s41592-023-02026-3) if you use our data and/or scripts in your studies.
## Index
### Pilot *in silico* mixture experiment
All scripts are available at [pilot](pilot) (Illumina) and [pilot_ONT/scripts](pilot_ONT/scripts) (ONT)
### Generate *in silico* mixture samples and preprocess
ONT: [ONT/mix_prepare](ONT/mix_prepare)
Illumina: [illumina/mix_prepare](illumina/mix_prepare)
### Generate downsampled samples and preprocess
Scripts are available at [downsample](downsample)
### Mapping and quantification
ONT: [ONT/preprocess](ONT/preprocess)
Illumina: [illumina/salmon_map.sh](illumina/salmon_map.sh)
### Quality control
ONT-specific: [ONT/QC](ONT/QC)
General: [longvsshort/overdisp.R](longvsshort/overdisp.R), [longvsshort/qc.R](longvsshort/qc.R) and [longvsshort/sequinCPMvsAbundance.R](longvsshort/sequinCPMvsAbundance.R)
### Isoform detection
Scripts to run softwares: [ONT/isoform_detection/methods](ONT/isoform_detection/methods)
Analysis of results: [ONT/isoform_detection/analysis](ONT/isoform_detection/analysis)
### Differential transcript expression
ONT: [ONT/DE_mix.Rmd](ONT/DE_mix.Rmd)
Illumina: [illumina/DE_mix.Rmd](illumina/DE_mix.Rmd)
Results comparison: [longvsshort/DEmixres.R](longvsshort/DEmixres.R)
### Differential transcript usage
ONT: [ONT/DTU_mix.Rmd](ONT/DTU_mix.Rmd)
Illumina: [illumina/DTU_mix.Rmd](illumina/DTU_mix.Rmd)
Results comparison: [longvsshort/DTUmixres.R](longvsshort/DTUmixres.R) and [longvsshort/DTUmixrestx.R](longvsshort/DTUmixrestx.R)