Computational tools

Raw data processing

Each read pair in a sequenced NTT-seq library contain an associated Tn5 barcode and a cell barcode. We recommend demultiplexing the reads based on the Tn5 barcode, so that you have separate FASTQ files for each Tn5 barcode (each corresponding to a different measured assay). You can then process the single-cell data using any tool used for scATAC-seq analysis, such as chromap or sinto.

Data analysis

Multimodal single-cell chromatin datasets can be analyze using the Signac R package. More information can be found at the Signac website and GitHub page.