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update readme with instructions to download data
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cmdoret committed Nov 15, 2018
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Expand Up @@ -13,9 +13,10 @@ In this project, we use restriction-site associated DNA-sequencing (RAD-seq) and
To run the pipeline with the data provided:

1. Download or clone this repository.
2. Download the `data` archive (not available yet) into the main folder
3. ```cd``` to the main folder
4. Untar the data using ```tar -xzvf data.tar.gz data```
2. Download the data archive from zenodo at: [https://zenodo.org/record/1488603#.W-1V9KBReLw]
3. Uncompress the downloaded file using ```tar xzvf 20181115_csd_data.tar.gz data``` and the resulting `data` folder to the root of the repository.
3. Download the gzipped fastq files from BioProject [PRJNA505237](https://www.ncbi.nlm.nih.gov//bioproject/PRJNA505237), on SRA (not available yet).
4. Move the RADseq files to `data/processed` and the WGS files to `data/wgs/raw/`.
5. Run the pipeline
1. On a cluster with LSF:
+ `make` to run the STACKS pipeline
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