https://github.com/mskcc/rediscoverte

Pipeline for quantifying genome-wide TE expression in RNA sequencing data
https://github.com/mskcc/rediscoverte

Last synced: 4 months ago
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Pipeline for quantifying genome-wide TE expression in RNA sequencing data

• Host: GitHub
• URL: https://github.com/mskcc/rediscoverte
• Owner: mskcc
• License: mit
• Created: 2024-07-01T17:44:15.000Z (almost 2 years ago)
• Default Branch: master
• Last Pushed: 2024-07-23T22:16:26.000Z (almost 2 years ago)
• Last Synced: 2026-01-26T14:22:31.138Z (5 months ago)
• Language: Nextflow
• Size: 188 KB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Citation: CITATIONS.md

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README

          
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## Introduction

**msk/rediscoverte** is a bioinformatics pipeline that quantifies genome-wide TE expression in RNA sequencing data. This is the nextflow pipeline for REdiscoverTE found here: https://github.com/ucsffrancislab/REdiscoverTE

1. Index transcriptome ([`Salmon Index`](https://combine-lab.github.io/salmon/getting_started/#indexing-txome))

2. Quantify reads ([`Salmon Quant`](https://combine-lab.github.io/salmon/getting_started/#quantifying-samples))

3. Run REdiscoverTE ([`REdiscoverTE`](https://github.com/ucsffrancislab/REdiscoverTE))

## Usage

> [!NOTE]

> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.

#### Running nextflow @ MSKCC

If you are runnning this pipeline on a MSKCC cluster you need to make sure nextflow is properly configured for the HPC envirornment:

```bash

module load java/jdk-17.0.8

module load singularity/3.7.1

export PATH=$PATH:/path/to/nextflow/binary

export SINGULARITY_TMPDIR=/path/to/network/storage/for/singularity/tmp/files

export NXF_SINGULARITY_CACHEDIR=/path/to/network/storage/for/singularity/cache

```

### Running the pipeline

First, prepare a samplesheet with your input data that looks as follows:

`samplesheet.csv`:

```csv

sample,fastq

SAMPLE_SINGLE_END,input_R1.fq.gz

```

Each row represents a fastq file (single-end) or a pair of fastq files (paired end).

Now, you can run the pipeline using:

```bash

nextflow run main.nf \

   -profile singularity,juno \

   --input samplesheet.csv \

   --outdir 

```

> [!WARNING]

> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;

> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).

## Credits

msk/rediscoverte was originally written by [nikhil](https://github.com/nikhil).

We thank the following people for their extensive assistance in the development of this pipeline:

## Contributions and Support

If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).

## Citations

> Kong, Y., Rose, C.M., Cass, A.A. et al. Transposable element expression in tumors is associated with immune infiltration and increased antigenicity. Nat Commun 10, 5228 (2019). https://doi.org/10.1038/s41467-019-13035-2

An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).

> **The nf-core framework for community-curated bioinformatics pipelines.**

>

> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

>

> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).