After sequencing, sequencing files should be run through the Parse Biosciences pipeline. The pipeline takes FASTQ files from both whole transcriptome and TCR sequencing and outputs a single report with summary statistics with key quality and performance metrics. UMAP plots with differential gene expression are available in addition to clonality analysis on the most frequent clones found in the experiment. Additional files output from the pipeline include digital gene expression matrices and T cell clone summaries following AIRR community data standards.
