Cellranger find which fastq file every cell belongs to
I have run cellranger on multiple fastq files that belong to different days and now I have output that can be read by Seurat but I need to know which time point every cell belongs to. To my knowledge none of the files in the outs directory of cellranger contain that information. Is there a way I can find out which fastq file every cell belongs to?
• 1,990 views
•
link
updated
by
Ram
•
written
by
Researcher •
•
written
by
Researcher •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Mapping FASTQ files of scRNA-seq to reference genome
written by Researcher •
-
sc-RNA seq pipeline
written by Researcher •
-
Separating a bam file into multiple bam files
written by Researcher •
-
Analyzing Single Cell Multiom ATAC Seq data (without Single Cell RNA Seq data) using SEURAT
written by halimaakhter014 •
-
Demultiplexing feature barcoded fastq files
written by s.sajib63 •
-
Sequencing file conversion
written by bill •
-
Demultiplexing 10x fastq files by GROUPS of barcodes
written by bds1217 •
-
Adding the csv file names as a separate column to the csv file
written by paramount.amin •
-
Can cell ranger count take a folder of only .fastq.gz as input?
written by jrleary
-
Finding genes that are differentially expressed directly or coming in later time points
written by zizigolu
What command did you use to run
cellranger? I think from memory, each fastq file will have 1 folder with matrix counts.I used the following commands, the fastq files were all stored in a single folder. I really like the way the current count matrix looks like with one count matrix for all files. Is there a way I can find out which fastq file every cell belongs to when I am reading the count matrix using Seurat?
Why did you delete the post, Researcher?
Please do not delete posts that have received feedback.