stats/generate_well_statistics
Description
Generate summary statistics from BAM files generated by STAR solo.
Arguments
Name | Type & Properties | Description |
|---|---|---|
--input | file | The .bam file as returned by the mapping tool STAR. |
--barcode | string required | The barcode for the well that is being processed. Is only used to add a metadata column to all output files. |
--well_id | string required | ID of this well. Only used to add a metadata column to the output files. |
--processedBAMFile | file output | Path to a .tsv file listing, per read in the BAM file, the value for the "CB", "UX", "GX" and "GN" tag, together with the chromsome to which the read was mapped to. |
--nrReadsNrGenesPerChrom | file output | Path to an output file that contains a .tsv formatted table describing per chromosome the number of reads that were mapped to that chromosome (NumberOfReads column) and the number of genes on that chromosome that had at least one read mapped to it (NumberOfGenes). |
--nrReadsNrUMIsPerCB | file output | Path to an output file that contains a .tsv formatted table describing per barcode the number of UMI's (nrUMIs) and the total number of reads (NumberOfReads). |
--umiFreqTop | file output | Path to an output file that contains a .tsv formatted table describing per UMI (column UB) the frequency at which they occur in the reads (column N). Only the top 100 UMIs are included. |
--threads | integer | Number of threads to use for decompressing BAM files. |
Run this component
Run the following command to execute this component with Nextflow:
cat > params.yaml <<'EOM'
processedBAMFile: "$id.$key.processedBAMFile"
nrReadsNrGenesPerChrom: "$id.$key.nrReadsNrGenesPerChrom"
nrReadsNrUMIsPerCB: "$id.$key.nrReadsNrUMIsPerCB"
umiFreqTop: "$id.$key.umiFreqTop"
threads: [ 1 ]
id: "run"
publish_dir: "output/"
EOM
nextflow run https://packages.viash-hub.com/vsh/htrnaseq.git \
-revision v0.15.0-rc.2 \
-main-script target/nextflow/stats/generate_well_statistics/main.nf \
-params-file params.yaml Relationships
Used by
1 relationships
Current component
stats/generate_well_statisticshtrnaseq v0.15.0-rc.2
Uses
0 relationships
No component dependencies found.