scHicDemultiplex (version 4.1)

Raw fastq file from Nagano 2017.:

barcode file:

Use GSE94489_README.txt file

SRR to Sample mapping file:

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

Buffer size:

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

Demultiplexing of raw fastq files

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. For other datasets, a third-party demultiplexing strategy must be used.

Afterwards, the demultiplexed mapped data can be used with HiCExplorer hicBuildMatrix to create single cell .cool matrices that must be stored in a .scool file using scHicMergeToSCool, in order to be used for downstream analyses in the scHiCExplorer suite.

For more information about scHiCExplorer please consider our documentation on readthedocs.io