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!
1 answer
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.
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