`dataset create`¶

Create one QuantNado .zarr store per sample from direct assay inputs.

Usage¶

quantnado dataset create \
  --sample RNA_1 \
  --assay RNA \
  --bamfile /data/RNA_1.bam \
  --stranded R \
  --output-dir dataset

Required Options¶

--sample: sample name
--assay: assay type
--output-dir, -o: directory for per-sample stores

Input Options by Assay¶

BAM-based assays (ATAC, ChIP, RNA, CUT&TAG, MCC) use --bamfile
METH uses --bamfile and --methylation_file
SNP uses --vcf_file
ChIP and CUT&TAG can also use --ip
RNA can also use --stranded

Supported Assays¶

ATAC
ChIP
RNA
CUT&TAG
METH
SNP
MCC

Options¶

--bamfile: BAM file for BAM-based assays and METH
--vcf_file: VCF file for SNP
--methylation_file: methylation bedGraph/TSV for METH
--ip: target label for ChIP / CUT&TAG
--stranded: RNA strandedness (R, F, 1, 2, U)
--chromsizes PATH: fallback .chrom.sizes file
--filter-chromosomes / --no-filter-chromosomes: keep only canonical chromosomes
--overwrite / --no-overwrite: replace an existing store
--chunk-len INTEGER: override position-axis chunk length
--construction-compression TEXT: one of default, fast, or none
--test: use the default test chromosomes (chr9, chr13, chr21)
--test-chrom TEXT: chromosome to keep in test mode; repeat to pass multiple chromosomes
--log-file PATH: log destination
--verbose, -v: debug logging

Examples¶

ATAC:

quantnado dataset create \
  --sample ATAC_1 \
  --assay ATAC \
  --bamfile /data/ATAC_1.bam \
  --output-dir dataset

ChIP:

quantnado dataset create \
  --sample H3K27ac_1 \
  --assay ChIP \
  --bamfile /data/H3K27ac_1.bam \
  --ip H3K27ac \
  --output-dir dataset

METH:

quantnado dataset create \
  --sample METH_1 \
  --assay METH \
  --bamfile /data/METH_1.bam \
  --methylation_file /data/METH_1.bedGraph \
  --output-dir dataset

SNP:

quantnado dataset create \
  --sample SNP_1 \
  --assay SNP \
  --vcf_file /data/SNP_1.vcf.gz \
  --output-dir dataset

Output¶

For --sample ATAC_1, QuantNado writes:

dataset/ATAC_1.zarr

Only completed stores are later included when you open a directory or combine stores.

dataset create¶