Anyone know which software or pipeline can treat the single-cell RNA-seq data from the first beginning? That means from the form of single or pair-end reads, and barcode, not matrix? The output should be tabulate reads and ready use for Seurat.
Thanks in advance for great help!
It would be beneficial to add what kind of single-cell data you have? There are a few different platforms/types and the raw data is not as simple as single/paired fastq files.
I will add to that.
Cellranger demultiplexed data is like that. Two read files and a separate file for index reads. You could just use
cellranger counts(links provided in other answers).
alevin(link) would also be a good solution.
Thank you so much for your great help!