FASTQ Processing

For data processed with the Illumina Single Cell 3’ RNA Prep Kit, each read in R1 includes a cellular barcode sequence followed by a 3-base binning index (BI) sequence. R2 includes the sequences cDNA constructs created from the captured mRNA, which contain random cut sites that serve as intrinsic molecular identifiers (IMIs) and are used for molecular counting.

For more information about FASTQ processing refer to the DRAGEN documentation detailing the DRAGEN PIPseq scRNA Pipeline.