Welcome to slide-seq-pipeline documentation!

slide-seq-pipeline This pipeline replicates most of the stuff provided in official slide-seq except the dependence to the google sheet and assumed internal file/folder location. We lack some of the generalization as these scripts are meant to run on a local machine. I would highly recommend installing the actual package since some of the functions are directly used in this repo.

Check out the Usage section for further information, including how to Installation the project.

Note

This project is under active development.

Contents

• Pipeline
  • Pre-requisite softwares
• Pipeline through notebooks
  • Preprocess output directory
  • Import the needed packages
    • Classes
    • Step 1 (Preparing for demultiplexing)
    • Step 2 Demultiplex (Has to be run in command line)
    • Step 3 Merge the barcode.unmapped ubams and
    • Step 4 recover whitelisted barcodes (Takes long run from command prompt)
  • Step 4a: Extract the barcodes (42bp) from the bam files
  • Step 4b: Create whitelist (Ideally one should borrow information from image analysis)
    • Step 5: Create the refined bam files
    • Step 6: Run the alignment step
    • Step 7: Run processing pipeline
• Recovery algorithm details
  • Bead Matrix
  • Current Algorithm
    • Index Building
    • Tuning the allowable rate