FastQC report analysis for scRNA seq data

Question

[aimanbarki]

Hello everyone, I downloaded healthy data set from the following website: BioProject_NCBI. I ran the Fast QC. This is how the results look like R1 vs R2:

Is it normal or R1 is really bad? How should i proceed next?

Thanks

Answer 1

[GenoMax]

It is likely not meaningful to do FastQC analysis of Read1 scRNAseq data. That read consists of cell barcodes and UMI's (~26-28 bp for 10x). Rest of the read can be just polyT etc, so that shows up as bad quality data. You should only check R2 data, if you are so inclined.

[aimanbarki]

GenoMax Thanks for the answer. But, it leads to another question i.e. Does Cellranger count automatically select the read its need to use. As we only provide the path to the fastq folder?

[GenoMax]

Cellranger will use the number of bases it needs from read 1 based on chemistry used.