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10x scRNAseq from just R1 and R2

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!

scrna alignment 10x
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updated by Ming Tommy Tang Ming Tommy Tang • written by ntsopoul • ntsopoul

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

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written by ntsopoul • ntsopoul

What was the cellranger command that you tried for counting?

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written by GenoMax GenoMax

2 answers

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/

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written by Ming Tommy Tang Ming Tommy Tang

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