stats/generate_well_statistics

Description

Generate summary statistics from BAM files generated by STAR solo.

Type

python_script

License

MIT

Links

Repository

Contributors

Launch

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 v0.14.7 \  
  -main-script target/nextflow/stats/generate_well_statistics/main.nf \  
  -params-file params.yaml

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.

Name

Type & Properties

--input

file

--barcode

string

required

--well_id

string

required

--processedBAMFile

file

output

--nrReadsNrGenesPerChrom

file

output

--nrReadsNrUMIsPerCB

file

output

--umiFreqTop

file

output

--threads

integer