scHicDemultiplex

scHicDemultiplex demultiplexes fastq files from Nagano 2017: “Cell-cycle dynamics of chromosomal organization at single-cell resolution” according their barcodes to a seperated forward and reverse strand fastq files per cell.

usage: scHicDemultiplex --fastq list of fastq files to demultiplex
                        [list of fastq files to demultiplex ...] --barcodeFile
                        list of fastq files to demultiplex. Use
                        GSE94489_README.txt file. --srrToSampleFile
                        SRRTOSAMPLEFILE [--outputFolder FOLDER]
                        [--threads THREADS] [--bufferSize BUFFERSIZE] [--help]
                        [--version]

Required arguments

--fastq, -f

The fastq files to demultiplex of Nagano 2017 Cell cycle dynamics of chromosomal organization at single-cell resolutionGEO: GSE94489. Files need to have four FASTQ lines per read:/1 forward; /2 barcode forward; /3 bardcode reverse; /4 reverse read.Please be aware the files can be downloaded via the command fastq-dump to be in the right format:fastq-dump –accession SRR5229025 –split-files –defline-seq ‘@$sn[_$rn]/$ri’ –defline-qual ‘+’ –split-spot –stdout SRR5229025 > SRR5229025.fastq

--barcodeFile, -bf

The fastq files to demultiplex

--srrToSampleFile, -s

The mappings from SRR number to sample id as given in the barcode file.

--outputFolder, -o

Path of folder to save the demultiplexed files

Default: “demultiplexed”

Optional arguments

--threads, -t

Number of threads. Using the python multiprocessing module.

Default: 4

--bufferSize, -bs

Number of lines to buffer in memory, if full, write the data to disk.

Default: 20000000.0

--version

show program’s version number and exit