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