Feature Counting

Feature counting is a technique to profile the expression of proteins (eg, cell surface proteins or antibodies). Feature reads differ from RNA reads because the read R2 is an oligo tag corresponding to a particular type of protein, and not a transcriptomic sequence.

To enable feature counting, specify the following command line options:

•

--scrna-feature-barcode-reference—Specify a CSV or FASTA feature reference file that contains feature barcodes.

•

--scrna-feature-barcode-groups—If feature reads are specified as separate FASTQ files, specify a comma-separated list of read groups that correspond to feature FASTQ files.

Output of feature counting is appended to the output expression matrix. The extended expression matrix contains additional rows corresponding to features.