baseqDrops

A versatile pipeline for processing dataset from 10X, indrop and Drop-seq.

See the beiseq/baseqDrops for details

System requirement

for efficient processing

• memory >= 30Gb
• CPU cores >=8

How to use

Before starting the container

• Desigante a folder for storing data files that will be mounted to the container, i.e. folder data

  mkdir data
  cd data
  

• Download and the reference genome from here

  # Curerent References - 3.0.0 (November 19, 2018)
  # Example - Human reference (GRCh38) 
  mkdir reference
  wget http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz
  tar xvzf refdata-cellranger-GRCh38-3.0.0.tar.gz
  

• Create the configuration file: ./create_config <genome> <container_path_to_reference_genome>

  # Example
  ./create_config hg38 data/reference/refdata-cellranger-GRCh38-3.0.0
  mv config_drop.ini data/
  

Run with volume

docker pull guoxindi/baseqdrops
# Example 
docker run -v -it "$(pwd)"/data:/usr/app/data guoxindi/baseqdrops run-pipe --config data/config_drop.ini -g hg38 -p 10X -n 10X_sample -1 data/input/10X_R1.fastq.gz -2 data/input/10X_R2.fastq.gz -d data/output

See beiseq/baseqDrops for details.