https://github.com/csoneson/wagneremt2020

https://github.com/csoneson/wagneremt2020

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• Host: GitHub
• URL: https://github.com/csoneson/wagneremt2020
• Owner: csoneson
• Created: 2020-07-08T14:01:18.000Z (over 4 years ago)
• Default Branch: master
• Last Pushed: 2021-02-04T13:50:34.000Z (almost 4 years ago)
• Last Synced: 2024-12-18T11:47:09.568Z (21 days ago)
• Language: R
• Size: 46.9 KB
• Stars: 0
• Watchers: 3
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# Mass Cytometric and Transcriptomic Profiling of Epithelial-Mesenchymal Transitions in Human Mammary Cell Lines

This repository contains the workflow for analyzing the RNA-seq data in 

* Wagner _et al_ (2021): Mass Cytometric and Transcriptomic Profiling of Epithelial-Mesenchymal Transitions in Human Mammary Cell Lines

The workflow structure is based on [`ARMOR`](https://github.com/csoneson/armor) ([Orjuela, Huang, Hembach _et al_, 2019](https://www.g3journal.org/content/9/7/2089.long)). To run the workflow and regenerate the results, follow the instructions below.

### Preparation

#### Download the data

The FASTQ files have been uploaded to ArrayExpress, with accession number [E-MTAB-9365](https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-9365/). Download the 32 FASTQ files, and place them in a subfolder named `FASTQ`.

#### Download the reference files

The analysis was performed using the Gencode v34 reference. Download the following files, unzip them, and place them in a subfolder named `reference_files`:

* genome: `ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/GRCh38.primary_assembly.genome.fa.gz`

* transcriptome: `ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.transcripts.fa.gz`

* gtf file: `ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_34/gencode.v34.annotation.gtf.gz`

#### Run the workflow

To run the workflow, first make sure that `snakemake` is available. Then, set up the conda environments:

```

snakemake --use-conda setup --cores 1

```

Check that all inputs are correctly specified:

```

snakemake --use-conda checkinputs --cores 1

```

Then you can run the full workflow as follows:

```

snakemake --use-conda --cores 16

```