Is it Possible to Filter a sc-RNA-Seq FASTQ based Upon Known Cell Barcodes?
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!
• 1,936 views
•
link
updated
by
swbarnes2
•
written
by
bioinformatics2020
•
written
by
bioinformatics2020
1 answer
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.
Log in to answer this question.
More posts like this
-
Submitting to GEO: 10x Fixed RNA profiling (Single Cell Gene Expression Flex)
written by psm
-
Filtlong and Flye
written by awhale01 •
-
Single cell Cluster based only perticular marker gene
written by luckysardar171 •
-
Appropriate tool to deconvolute complex Sanger chromatograms in order to retrieve specific DNA barc…
written by l.beumers •
-
scRNA: subset a small number of fastq reads
written by bsmith030465
-
Hierarchical Clustering of Single-Cell Counts
written by bioinformatics2020
-
How to find percentage of a gene (eg.Ppbp) for condition A and condition B from 10X Single Cell RNA…
written by bioinforesearchquestions
-
scRNAseq: Split FASTQ into cell specific FASTQ Files
written by niklas.lang •
-
Analyzing MARS-seq (single-cell RNA seq) fastq files
written by Eldad Shulman •
-
Tools for demultiplexing a large fastq file based on random in-line barcodes
written by alyssamolinaro91 •
Is this 10x data?
Yes, the FASTQ files are 10X datasets.
This is a list of codes 10x BAM files use. It should be possible to use your list to get the reads you need.