How to produce count matrix with multiple run files?

Question

[Athena]

After converting sra files to fastq files, do I need to run each fastaq files via 10X CellRanger program individually can it run multiple fastq files in one-go producing a count matrix? The sra has 6 runs so 6 different accession number each which results in 6 fastq files.

Trying to learn this all by myself before starting an internship so Im sorry if I am asking a newbie question.

Answer 1

[Antonio R. Franco]

The usual way to go is to run individually each of your samples generating different directories with the counts, and then combine all the individual directories with the counts afterwards. You should use a design table to define the conditions (factors)

[Athena]

Ok so I shouldn't follow the 10X instruction then. Link: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/tutorial_ct

It looks like they run the same sample, eventhough it has different lanes (L0001&L002), they just run it all together. The data im trying to use is from same sample but different lanes, each lane as individual sra/fastq file. So should I still run it separately just to be on the safe side?

[Antonio R. Franco]

I don't see the point of mixing different samples when you are running a single-cell experiment. I've been reading the tutorial, and ended reading this

If there is more than one sample in the FASTQ directory, use the --sample argument to specify which samples to use. This --sample argument works off of the sample id at the beginning of the FASTQ file name