cell ranger low correct barcodes and failed

Question

[shersky]

I downloaded single nuclei RNA sequencing data by different methods fastq-dump/prefetch/fasterq-dump and it always resulted in 4 files I1,I2,R1 and R2

I downloaded the following accessions

• SRR21834805
• SRR21834806

I put the 8 files in one directory and ran cell ranger and the cellranger count attempts failed as it detected low rate of correct barcodes. the error is below:

An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input: Sample 6438-RMM-0002_12 in "/tmp/4481_rep2". Please check your input data.
- 1.2% for chemistry SC3Pv3
- 1.2% for chemistry SC3Pv3HT
- 0.1% for chemistry SC5P-R2
- 0.1% for chemistry SC3Pv2
- 0.0% for chemistry SC3Pv3LT

library prep was 10x single cell multiome. is this why it is not working?

On ENA it is just one fastq file. How do I convert it into R1 and R2?

[shersky]

@GenoMax can you please take a look?

[GenoMax]

library prep was 10x single cell multiome

Are you trying plain cellranger? You need to use cellranger-arc software: https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/using/count

[shersky]

would cellranger-arc work only on the fastq files of the snRNA of the study? They have different SRA accessions for the snATAC and the snRNA. how will this work?

[GenoMax]

You need to provide both sample types to cellranger-arc at the same time. Please check the link posted above. This data needs to be analyzed together with arc.