Demultiplex Fastqs at level of single cell

[sevans625]

I was wondering if there was a tool for demultiplexing scRNAseq fastqs at the level of single cell, so that I have one fastq files for each cell in my data set. This will allow me to have the proper input for your program.I am working with data generated with 10x genomics platform, so all cells are in one fastq right now.

Thanks!

[fobinf]

Dear sevans625,

10X surely have a demultiplexing system, but it is usually used inside the black box of cellRanger. I think I would use that for initial analysis, saving you some effort. CellRanger is demultiplexing and then using STAR for alignment. When you have the expression matrix you can look into using our pipeline qc analysis. I think this will get you faster to the fun part of you analysis. 10X was not a thing when we developed this pipeline, so faster approaches exists for that type of data.