qc/calculate_atac_qc_metrics
Description
Add basic ATAC quality control metrics to an .h5mu file.
The metrics are comparable to what scanpy.pp.calculate_qc_metrics output,
although they have slightly different names:
Obs metrics (name in this component -> name in scanpy):
n_features_per_cell -> n_genes_by_counts
total_fragment_counts -> total_counts
Inputs
Name | Type & Properties | Description |
|---|---|---|
--input | file required | Input h5mu file |
--fragments_path | file | Path to the fragments file. If not provided and not present in the input h5mu file, the nucleosome signal and TSS enrichment score will not be calculated. |
--modality | string | |
--layer | string | Layer at `.layers` to use for the calculation. If not provided, `.X` is used. |
--n_fragments_for_nucleosome_signal | integer | Number of fragments to use per cell for nucleosome signal calculation. Takes very long to calculate, for a test run lower value (e.g. 10e3) is recommended. See https://www.sc-best-practices.org/chromatin_accessibility/quality_control.html#nucleosome-signal for more information |
--nuc_signal_threshold | double | Threshold for nucleosome signal. Cells with nucleosome signal above this threshold will be marked as low quality ("NS_FAIL"), otherwise they will be marked "NS_PASS". |
--n_tss | integer | Number of the transcription start sites to calculate TSS enrichment score. See https://www.sc-best-practices.org/chromatin_accessibility/quality_control.html#tss-enrichment for more information |
--tss_threshold | double | Threshold for TSS enrichment score. Cells with TSS enrichment score below this threshold will be marked as low quality ("TSS_FAIL") otherwise they will be marked as "TSS_PASS". |
Outputs
Name | Type & Properties | Description |
|---|---|---|
--output | file output | Output h5mu file. |
--output_compression | string | The compression format to be used on the output h5mu object. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
modality: [ "atac" ]
n_fragments_for_nucleosome_signal: [ 100000 ]
nuc_signal_threshold: [ 2 ]
n_tss: [ 3000 ]
tss_threshold: [ 1.5 ]
output: "$id.$key.output.h5mu"
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \
-revision 2.1.2 \
-main-script target/nextflow/qc/calculate_atac_qc_metrics/main.nf \
-params-file params.yaml Relationships
Used by
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Current component
qc/calculate_atac_qc_metricsopenpipeline 2.1.2
Uses
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