This is a name for output files, for example Experiment1_Metrics_Summary.csv. Default if left empty is to name run based on a library. Any non-alpha numeric characters will be changed to a hyphen.

Specify the Sample Tag number followed by - (hyphen) and a sample name to appear in the output files. For example: 4-Ramos. Should be alpha numeric, with + - and _ allowed. Any special characters: &, (), [], {}, <>, ?, | will be corrected to underscores.

The VDJ species and chain types. This option should only be set for VDJ experiment.

Default: false. A Bam read alignment file contains reads from all the input libraries, but creating it can consume a lot of compute and disk resources. By setting this field to true, the Bam file will be created.

The maximum number of threads to use in the pipeline. By default, all available cores are used.

Set a specific number (>=1) of cells as putative, based on those with the highest error-corrected read count

The e-value threshold for J gene call by IgBlast/PyIR, default is set as 0.001

The e-value threshold for V gene call by IgBlast/PyIR, default is set as 0.001

Specify the data to be used for putative cell calling. mRNA is the default selected option.

Optional. Guide the basic putative cell calling algorithm by providing an estimate of the number of cells expected. Usually this can be the number of cells loaded into the Rhapsody cartridge. If there are multiple inflection points on the second derivative cumulative curve, this will ensure the one selected is near the expected.

The sample multiplexing kit version. This option should only be set for a multiplexed experiment.

By default, reads aligned to exons and introns are considered and represented in molecule counts. Including intronic reads may increase sensitivity, resulting in an increase in molecule counts and the number of genes per cell for both cellular and nuclei samples. Intronic reads may indicate unspliced mRNAs and are also useful, for example, in the study of nuclei and RNA velocity. When set to true, intronic reads will be excluded.

By default, putative cells are determined using only the basic algorithm (minimum second derivative along the cumulative reads curve). The refined algorithm builds on the basic cell call, by analyzing expression patterns to remove false positives and recover false negatives. The refined algoritm may not be suitable for noisy datasets, and certain mixtures of cell types. Does not apply if Exact Cell Count is set.