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Selecting Keep untrimmed will generate a separate unaligned reads data node with any reads that do not match the structure specified by the prep kit. This option is off by default, to save on disk space. Selecting Map feature barcodes is only necessary for processing protein data from 10X 10x Genomics' Feature Barcoding assay (v3+ chemistry). For single cell gene expression data, leave this option unchecked.
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Like adaptors, barcodes can be specified using a file or manually specified, but you can also choose to designate any a segment of arbitrary length in the sequence as the barcode. This is useful if you do not have a specific set of known barcodes.
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