Question: Does Cell Ranger DNA match and trim barcodes like Long Ranger or Cell Ranger?
Answer: Both Long Ranger and Cell Ranger DNA both use the first 16 bases of Read 1 to identify and trim the 10x Barcode.
Long Ranger also trims the subsequent 6 bases due to the presence of the hexamer in this location that was used for genome amplification, and one extra base that tends to have a lower sequencing quality. By contrast, Cell Ranger DNA does not trim the random hexamer sequences that were used in genome amplification.
Chromium Single Cell DNA library construct:
Trimming the hexamer (+1) sequence is important for Long Ranger due to the single nucleotide variant detection that is done. Any mismatches between the random hexamer and the primer binding site during amplification would be maintained in the final product, which would lower the specificity of variant detection.
Chromium Single Cell DNA libraries also use random oligo sequences for amplification, however the data type required for the CNV application is read counts, not nucleotide level sequence information. Therefore Cell Ranger DNA does not trim the hexamer sequences from Chromium Single Cell DNA libraries.