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gtars-fragsplit

Split fragment files according to pseudobulk assignments for single-cell ATAC-seq data processing.

Features

Section titled “Features”
  • Efficient fragment file splitting
  • Pseudobulk generation from single-cell data
  • Support for cell type annotations
  • Gzip compression support
  • Memory-efficient streaming

Usage

Section titled “Usage”

Command Line

Section titled “Command Line”
Terminal window
gtars fragsplit \
  --fragments fragments.tsv.gz \
  --barcodes barcodes.txt \
  --output-dir pseudobulk/

From Python

Section titled “From Python”
from gtars import fragsplit


fragsplit.split_by_clusters(
    fragments="fragments.tsv.gz",
    clusters="clusters.csv",
    output_dir="pseudobulk/"
)

Input Formats

Section titled “Input Formats”

Fragment File

Section titled “Fragment File”

Standard 10x Genomics format:

chr1    1000    1500    AAACCCAAGAAACACT-1    1

Barcode Assignment

Section titled “Barcode Assignment”
AAACCCAAGAAACACT-1    cluster1
AAACCCAAGAAACAGC-1    cluster2

Output

Section titled “Output”

Creates one fragment file per cluster/pseudobulk group with appropriate cell barcodes.