I am new to single cell (SC) RNA-Seq and have a rather naive q regarding the alignment of single cell fast q files. As, there are hundreds/thousands of fast q files corresponding to their respective SCs, How do we align all these fastq files in parallel? should one align a few fastq files at a time or all these (hundreds/thousands of fast q files) all at once in some aligner? (Hisat/STAR). What is the preferred method? Is there any online instruction available regarding this (I didn't find anything addressing this specifically, that why I think its probably too naive) I am fairly conversant with bulk sequencing methods so any link to a fairly basic but recent workflow would be a great help.
PS: I am working with about 4k publicly available cancer single cell fast q files.