cellranger outcome

Question

[Andy]

Good morning, everyone!

I have a question about my Cell Ranger results. As the dataset I used is a single-cell RNA sequencing study and only provides BAM files, I successfully converted the BAM file to FASTQ files using the "bamtofastq" command. However, upon receiving my Cell Ranger results for the FASTQ files, I noticed that the results did not look good for low fraction reads in cells. I remember reading somewhere that a median gene per cell lower than 700 may cause clustering problems. I am wondering if I should re-run the Cell Ranger analysis and add the command "force-cell=xxx." My concern is that this may cause me to unevenly lose some cells across different cell clusters. Or will it not solve my problem. Thanks in advance!

Answer 1

[swbarnes2]

The fact that this wasn't a complete failure just about proves that you didn't do anything wrong in going back to fastq and reprocessing.

This is almost certainly not a processing issue, it's what the library actually looks like, and bioinformatics fiddling can't fix that.

[Andy]

Thanks! Yeah, I am hesitant about whether I should include this data in my study or not. Do you have any suggestions?