10x scRNAseq from just R1 and R2

Question

[ntsopoul]

Hi,

we performed 10x library prep for scRNAseq analysis. I received from our facility the already de-multiplexed fastq files (Read1 and Read2) via bcl2fastq. However, no index file is included since they do not have cellranger installed. Is it possible to get to the count matrix just with the read1 and read2? How do I do this? I tried to feed the data into cellranger but with no success.

Thanks!

[GenoMax]

Index files are optional in certain types of count situations (see https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/fastq-input ). Is this 3' gene expression data or something else?

[ntsopoul]

thanks, it is indeed 3' gene expression. How would you recommend I proceed?

[GenoMax]

What was the cellranger command that you tried for counting?

Answer 1

[Ming Tommy Tang]

The I1 index fastq is optional. see my post https://divingintogeneticsandgenomics.rbind.io/post/understand-10x-scrnaseq-and-scatac-fastqs/

you can use https://salmon.readthedocs.io/en/latest/alevin.html

salmon alevin -l ISR -1 cb.fastq.gz -2 reads.fastq.gz --chromium -i salmon_index_directory -p 10 -o alevin_output --tgMap txp2gene.tsv

or kb_python https://www.kallistobus.tools/kb_usage/kb_usage/

Answer 2

[ATpoint]

This is a FAQ at 10x: https://kb.10xgenomics.com/hc/en-us/articles/360004982791-Does-Cell-Ranger-need-the-I1-FASTQ-file-to-run-