How do I decrease or increase the UMI threshold used to remove bead barcodes?
How do I decrease or increase the UMI threshold used to remove bead barcodes?
- The use of --bb_min flag during Seeker pipeline execution may be utilized to lower the default UMI cutoff of 10. Here is an example of the Seeker pipeline execution command with the UMI cutoff set to seven (this overrides the default of 10):
nextflow run main.nf \
--input /path/to/samplesheet.csv \
--outdir ${root_output_dir}/results/ \
-work-dir ${root_output_dir}/work/ \
--igenomes_base /path/to/references/ \
--bb_min 7 \
-profile singularity