Single cell RNA-Seq barcode error correction

User Guide

Get help information

bash correct_barcode.sh -h

./correct_barcode.sh [options]

-h --help

Please specify the following options:

-fq1 --fastq_cell=SRR1853178_1.fastq [gzipped or plain fastq R1 cell index reads]

-fq2 --fastq_biology=SRR1853178_2.fastq [gzipped or plain fastq R2 biology reads]

-bcs --bc_start=1 [start position of cell barcode in cell index reads]

-bcl --bc_length=12 [length of cell barcodes in cell index reads, 12 for dropseq data, 16 for 10XGv2,v3 data]

-t --threads=8 [number of threads to use]

-o --output=BCFIX [output file name]

-w --whitelist=NO [whitelist of barcodes, optional for 10XG data]

An example to run the program on a 10XGv2 dataset

bash barcode_correct4.sh -fq1=hgmm_6k_R1.fastq.gz -fq2=hgmm_6k_R1.fastq.gz -bcs=1 -bcl=16 -t=8 -o=BCFIX -w=10Xv2_whitelist.txt