tw7649116 / haplotyped-methylome Goto Github PK

Reproducibility instructions for Gigante et al., 2018.

Note: this repository is still being tested! If you find a bug, please file an issue.

Data available at ENA Accession PRJEB27157.

• R
• Python>=3.5
• Lots of RAM (min 256GB)
• Lots of disk space (estimate: 2TB)

To install with conda, run the following command.

conda env create -f environment.yml
source activate haplotyped_methylome

You will then need to install Albacore: it is available on the Nanopore Community.

To install without conda, see the list of dependencies at the bottom of this README.

For the standard workflow, snakemake will download all the necessary files.

If you wish to avoid running albacore, bwa and nanopolish on the raw nanopore data, you can run the following command, which downloads the output of these programs and tricks snakemake into thinking you have run the pipeline from the beginning:

snakemake intermediate_download

Note: the download link for these files is not yet available, but will be posted to ENA shortly.

If you wish to rerun from the beginning after running this command, you can revert to the original download with snakemake --forceall.

To generate all plots, tables and notebooks, simply run from the root directory:

snakemake --cores 16

If you don't wish to run the full analysis, you can run specific rules from the Snakefile by running, for example:

snakemake --cores 16 rnaseq_analysis
snakemake --cores 16 haplotype_analysis
snakemake --cores 16 methylation_analysis

Software dependencies:

• SAMtools
• Hisat2
• Trim Galore
• SNPsplit
• Bismark
• Bowtie 2
• Pandoc
• Albacore (optional)
• BWA (optional)
• Nanopolish (optional)

Python package dependencies:

pip install --user -r requirements.txt

R package dependencies:

Rscript install_R_deps.R

• rnaseq_analys.Rmd failed: there is no package called 'ggrastr'

If devtools doesn't play nicely with conda, sometimes the automatic GitHub installation of ggrastr fails. You can resolve if as follows:

git clone --depth 1 https://github.com/VPetukhov/ggrastr.git
cd ggrastr
R -e 'devtools::install()'