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Instructions SNS

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javrodriguez edited this page Dec 12, 2023 · 5 revisions
  1. Download repository.

module load git

git clone https://github.com/javrodriguez/DBIND

  1. Create symlinks to input data.

cd DBIND

ln -sn ../BAM-DD ./

ln -sn ../peaks-MACS-broad-q-0.05 ./PEAK-DIR

ln -sn ../summary-combined.chip.csv ./

ln -sn ../summary.peaks-macs-broad-q-0.05.csv ./

  1. Create sample sheet

module load r

Rscript ./make_sampleSheet.R

  1. If there are samples for different different factors (i.e. different TFs or chromatin marks) and/or cell lines, fill the columns Factor and Tissue in the table samples.diffBind.csv accordingly.

  2. Make PCAs.

sbatch pca_diffBind.sh

  1. Combine stats.

./combine_stats.sh

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