10k-ft-overview-seqc

10,000-ft Overview of SEQC

Code Overview

Main Function

run.py

def run(args) -> None:
  ...

Program Arguments

args

Platform

Platform-specific code

• 10x v2
• 10x v3
• InDrop
• ...

Determine Starting Point

• From FASTQ (.fastq)
• From aligned BAM (.bam)
• From ReadArray object (.h5)

Download

• Inputs

Merge FASTQ

• READ1 + READ2

Alignment

• Internally using STAR

Creating ReadArray Object

• H5 object
• Explore the ReadArray object
  • pysam and pyranges are not required for exploring ReadArray object, but required for BAM/GTF lookup.

Cell Barcode Correction

Resolve Ambiguous Alignments

• Multimapping

UMI Correction

• Dask

Sparse Count Matrix

• mtx and csv

Filtering

• Four filters

Dense Count Matrix

• csv

Development/Debug Environment

• Local (can't do with a big dataset)
  • Visual Studio Code
  • PyCharm
• Remote
  • HPC (e.g. pdb)
  • AWS (e.g. Cloud9, VS Code in the browser)

Setting Up Dev Envionrment

https://github.com/dpeerlab/seqc/blob/master/docs/install-dev.md

Testing & CI/CD

https://github.com/dpeerlab/seqc/blob/master/docs/run-test.md

• nosetest
• CicleCI
• GitHub Actions

Packaging

• Docker
• Packer
• WDL