hashtag

This directory includes hashtag_tool executable to process single-cell hashtag data (tested on Ubuntu 18.04).

USAGE:

hashtag_tool [OPTIONS]

FLAGS:
-h, --help Prints help information
-V, --version Prints version information

OPTIONS:
--R1 R1 raw fastq file (doesn't work for *gz file)
--R2 R2 raw fastq file (doesn't work for *gz file)
--bc_len <barcode_len> the length of barcodes
--bc A list of cell barcodes
--ft A list of hashtag barcodes
--hashtag_len <hashtag_len> the length of hashtag
--umi_len <umi_len> the length of UMI

Quick start:

hashtag_tool --R1 R1.fastq --R2 R2.fastq --bc barcodes.txt --ft hashtag.txt --bc_len 16 --umi_len 12 --hashtag_len 15

The output matrix file is called ft_count.txt