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EXAMPLES.md

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Pipeline examples

Quick start: InDrop v3 mouse data

To run the pipeline on the small subset of inDrop Mouse BMCs, use the following commands.

Go to the script directory:

cd dropEst/examples/scg71_demo

Download data and prepare structure of the folders:

make

Run the pipeline, using STAR aligner. It requires you to have STAR and zcat in the PATH:

./pipeline.sh path_to_dropest_binaries path_to_config path_to_star_index path_to_genes_gtf

Here:

  • path_to_dropest_binaries - path to the folder with dropest and droptag binaries;
  • path_to_config: path to indrop_v3.xml config;
  • path_to_star_index: path to STAR index;
  • path_to_genes_gtf: path to gtf file with annotated genes.

Example:

./pipeline.sh ~/dropEst/build ~/dropEst/configs/indrop_v3.xml /n/groups/pklab/genomes/mm10/STARIndex /n/groups/pklab/genomes/mm10/genes.gtf

The following command downloads mm10_genes.gtf, which was used by the authors:

make genes

To examine validity of the results, you can download whole snapshot of the folder, which we got by running the same commands. The following command downloads them to results folder:

make results