Cellranger find which fastq file every cell belongs to
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19 months ago
Researcher ▴ 20

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?

scrnaseq cellranger fastq sequencing seurat • 1.2k views
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Why did you delete the post, Researcher?

Please do not delete posts that have received feedback.

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What command did you use to run cellranger? I think from memory, each fastq file will have 1 folder with matrix counts.

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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?

cellranger-7.0.1/bin/cellranger count \
--id=run_files \
--fastqs=/data/ \
--sample=E \
--transcriptome=/yard/run_cellranger_count/refdata-gex-GRCh38-2020-A
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