maximum number of mismatches allowed in adapter sequence.

adapter sequence to anchor barcodes.

length of the barcode read

cell barcode length

matching the Cell Barcodes to the WhiteList

position of Cell Barcode(s) on the barcode read. Presently only works with --soloType CB_UMI_Complex, and barcodes are assumed to be on Read2. Format for each barcode: startAnchor_startDistance_endAnchor_endDistance start(end)Anchor defines the anchor base for the CB: 0: read start; 1: read end; 2: adapter start; 3: adapter end start(end)Distance is the distance from the CB start(end) to the Anchor base String for different barcodes are separated by space. Example: inDrop (Zilionis et al, Nat. Protocols, 2017): --soloCBposition 0_0_2_-1 3_1_3_8

cell barcode start base

file(s) with whitelist(s) of cell barcodes. Only one file allowed with

cell filtering type and parameters

genomic features for which the UMI counts per Cell Barcode are collected

file names for STARsolo output. default: file_name_prefix gene_names barcode_sequences cell_feature_count_matrix

type of single-cell RNA-seq

strandedness of the solo libraries

type of UMI deduplication (collapsing) algorithm

type of UMI filtering

UMI length

position of the UMI on the barcode read, same as soloCBposition Example: inDrop (Zilionis et al, Nat. Protocols, 2017): --soloCBposition 3_9_3_14

UMI start base