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indrops-star

Pipeline to analyze Indrops V3 data using STARsolo

Installation

Clone this repository

git clone https://github.com/BradhamLab/indrops-star/

Install conda environment

conda env create -f environment.yml

Run Pipeline

Edit Configuration File

The indrops-star uses a configuration file files/config.yaml. Modify the empty example configuration file files/empty_config.yaml in your local clone to suit your needs. Entries are explained below:

genome:
  fasta: "your/genoma/sequences.fasta" # file path to genome fasta file
  gtf: "your/genome/annotations.gtf" # file path to genome annotations as gtf file
STAR:
  index: "star/index/install/dir" # where to build STAR index
project:
  dir: "head/of/your/project/dir/Intensities/Basecalls"  # directory containing fastq files
  id: "your-project-id"  # project identification string
  libraries:  # key value mapping library barcodes to library names
    {"ATTAGAGG": "Library1", # Index was CCTCTAAT, reverse compliment: ATTAGAGG
     "CGGAGAGA": "Library2", # Index was TCTCTCCG <==> CGGAGAGA
     "CTAGTCGA": "Library3", # Index was TCGACTAG <==> CTAGTCGA
     "AGCTAGAA": "Library4"} # Index was TTCTAGCT <==> AGCTAGAA
params:
  weave_fastqs:
    mismatches: 2  # allowable mismatches in library barcodes
  star_index: "--sjdbOverhang 60 --genomeSAIndexNbases 13" # put extra STAR parameters to pass when building index here
  star_solo: "--soloCBmatchWLtype 1MM_multi" # put extra STAR alignment parameters here

Run Pipeline using snakemake

From the head of the repo, execuate the pipeline by issueing the following command:

conda activate indrops-star
snakemake

Final STARsolo output will be found in <your/project/dir>/processed/STAR/

For more information on Snakemake see the documentation for more information.