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https://github.com/jdblischak/midway-subread-pipeline
Process RNA-seq data with Subread on RCC Midway
https://github.com/jdblischak/midway-subread-pipeline
bioconductor rna-seq
Last synced: 20 days ago
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Process RNA-seq data with Subread on RCC Midway
- Host: GitHub
- URL: https://github.com/jdblischak/midway-subread-pipeline
- Owner: jdblischak
- License: cc0-1.0
- Created: 2017-07-17T18:30:17.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2017-09-14T02:42:59.000Z (over 7 years ago)
- Last Synced: 2024-10-15T23:55:26.547Z (2 months ago)
- Topics: bioconductor, rna-seq
- Language: R
- Size: 10.7 KB
- Stars: 2
- Watchers: 3
- Forks: 2
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# Midway Subread pipeline
These scripts process RNA-seq data using the [Subread][] pipeline. The
scripts are designed to be used with the [Slurm scheduler][slurm] on
the [RCC Midway2][midway] cluster at the University of Chicago, but
can be adapted to other computing infrastructure.
## Setup
1. Install the R/Bioconductor packages [biomaRt][] and [Rsubread][]:
```r
source("https://bioconductor.org/biocLite.R")
biocLite(c("biomaRt", "Rsubread"))
```
2. Clone this repository with `git clone` or download and unzip this
[zip file][master].
## Pipeline
The scripts should be submitted in the following order. Always run
them from the head node in the root of the project directory.
1. Download and index the genome with `download-genome.R`:
```bash
sbatch --mem=12G --partition=broadwl download-genome.R
```
2. Download and format the exons with `download-exons.R`:
```bash
sbatch --mem=2G --partition=broadwl download-exons.R
```
3. Submit mapping jobs with `submit-subread.sh`, which calls
`run-subread.R` for each fastq file:
```bash
bash submit-subread.sh
```
4. Submit counting jobs with `submit-subread.sh`, which calls
`run-featurecounts.R` for each BAM file:
```bash
bash submit-subread.sh
```
## Directory structure
These scripts expect the following directory structure. Only `fastq/`
has to be created manually. The scripts will create `bam/`, `counts/`,
and `genome/`.
```
.
├── bam
├── counts
├── fastq
│ ├── YG-172S-S8-8_S125_L006_R1_001.fastq.gz
│ └── YG-172S-S8-9_S126_L006_R1_001.fastq.gz
└─── genome
```
* `fastq/` - Contains raw data in `fastq.gz` files.
* `bam/` - Contains the mapped reads in BAM files.
* `counts/` - Contains the read counts in text files.
* `genome/` - Contains the index genome and the exons coordinates in
SAF format.
## License
The code is available under the [CC0 license][cc0], i.e. you are free
to do whatever you like with this code, but it comes with no
guarantees. See the file `LICENSE` for full details.
## More information
* [RCC User Guide][guide]
* [Gilad Lab Midway Guide][giladlab]
[biomaRt]: https://bioconductor.org/packages/release/bioc/html/biomaRt.html
[cc0]: https://creativecommons.org/share-your-work/public-domain/cc0/
[guide]: https://rcc.uchicago.edu/docs/
[giladlab]: https://github.com/jdblischak/giladlab-midway-guide
[master]: https://github.com/jdblischak/midway-subread-pipeline/archive/master.zip
[midway]: https://rcc.uchicago.edu/resources/high-performance-computing
[Rsubread]: https://bioconductor.org/packages/release/bioc/html/Rsubread.html
[slurm]: https://slurm.schedmd.com/
[Subread]: http://subread.sourceforge.net/