Calculate atac qc metrics
Add basic ATAC quality control metrics to an .h5mu file.
Info
ID: calculate_atac_qc_metrics
Namespace: qc
Links
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
Example commands
You can run the pipeline using nextflow run
.
View help
You can use --help
as a parameter to get an overview of the possible parameters.
nextflow run openpipelines-bio/openpipeline \
-r 2.1.0 -latest \
-main-script target/nextflow/qc/calculate_atac_qc_metrics/main.nf \
--help
Run command
Example of params.yaml
# Inputs
input: # please fill in - example: "input.h5mu"
# fragments_path: "fragments.tsv.gz"
modality: "atac"
# layer: "raw_counts"
n_fragments_for_nucleosome_signal: 100000
nuc_signal_threshold: 2.0
n_tss: 3000
tss_threshold: 1.5
# Outputs
# output: "$id.$key.output.h5mu"
# output_compression: "gzip"
# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
# Arguments
nextflow run openpipelines-bio/openpipeline \
-r 2.1.0 -latest \
-profile docker \
-main-script target/nextflow/qc/calculate_atac_qc_metrics/main.nf \
-params-file params.yaml
Note
Replace -profile docker
with -profile podman
or -profile singularity
depending on the desired backend.
Argument groups
Inputs
Name | Description | Attributes |
---|---|---|
--input |
Input h5mu file | file , required, example: "input.h5mu" |
--fragments_path |
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. | file , example: "fragments.tsv.gz" |
--modality |
string , default: "atac" |
|
--layer |
Layer at .layers to use for the calculation. If not provided, .X is used. |
string , example: "raw_counts" |
--n_fragments_for_nucleosome_signal |
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 | integer , default: 100000 |
--nuc_signal_threshold |
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”. | double , default: 2 |
--n_tss |
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 | integer , default: 3000 |
--tss_threshold |
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”. | double , default: 1.5 |
Outputs
Name | Description | Attributes |
---|---|---|
--output |
Output h5mu file. | file , example: "output.h5mu" |
--output_compression |
The compression format to be used on the output h5mu object. | string , example: "gzip" |