Cellranger pipeline 3.1.0 demultiplexing (cellranger demux)

Question

[Emily]

I'm trying to run cellranger 3.1.0 demux command for flowcell fastq files but keep running into problem where when I run the command cellranger demux --run=/pathway/to/fastq/file/directory it doesn't process the fastq files. I'm not sure if I need to do additional steps/set parameters. I even tried cellranger demux --fastqs=/pathway/to/fastq/directory but still run into the error. I'm not too familiar with this old cellranger pipeline version so any help would be much appreciated. Thank you

The fastq file source:https://www.10xgenomics.com/resources/datasets/6-k-pbm-cs-from-a-healthy-donor-1-standard-1-1-0 when I download their fastq files (.tar) and decompressed it created .../fastqs/flowcell1 directory

The documentation that 10X support had me refer to: https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/using/fastq-input (under "Scenario: My FASTQs are named like "read-I1-AAAAAAA_lane-001-chunk-001.fastq.gz")

Answer 1

[ATpoint]

https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/demultiplex

The cellranger demux pipeline is the first step in analyzing a Chromium sequencer run. It takes an Illumina BCL output folder and demultiplexes based on the 8bp sample index read, and generates FASTQs for the R1 and R2 paired-end reads as well as the sample index.

demux does not accept fastq, it produces fastq from bcl. What you see is perfectly expected.

[Emily]

Got it, thank you. How do I run the cell ranger count for those types of file? The file names are not the conventional format so those don't run on cellranger version 3+