Is it Possible to Filter a sc-RNA-Seq FASTQ based Upon Known Cell Barcodes?

Question

[bioinformatics2020]

I have a single-cell FASTQ file (made up of roughly 500,000 unfiltered cells), and then a list of about 10,000 filtered barcodes. I was curious if there was any way to filter the original FASTQ so only reads that are originating from these 10,000 barcodes remain. Is there any possible way of doing this?

Cheers!

[GenoMax]

Is this 10x data?

[bioinformatics2020]

Yes, the FASTQ files are 10X datasets.

[GenoMax]

This is a list of codes 10x BAM files use. It should be possible to use your list to get the reads you need.

Answer 1

[swbarnes2]

If you filter the fastqs themselves based on cell barcodes, you will miss one offs, unless you are careful. (You could use umi_tools whitelist to get a list of the one-offs)

What you might do instead is put the whole thing through cellranger, and then cellranger reanalyze can take a list of barcodes and redo the later steps of the analysis with just those barcodes.