low Reads Mapped Confidently to Transcriptome?

[dm8000]

Hello

I ran the cellranger count function to align a fastq file to two different genomes. I followed the tutorial without changing parameters. However, in one report I got only 45% of Reads Mapped Confidently to Transcriptome, while in the other I got 67%. I assume these values are low. On the other hand, 96% of the reads were aligned with the genome. Additionally, a colleague aligned the same dataset with the same parameters and got a higher number of mean reads per cell. We both used the human genome provided by cellranger.

What could this value of Reads Mapped Confidently to Transcriptome mean? Is there a problem with the way I ran it, or is it a biological problem?

[evolvedmicrobe]

If you align the same FASTQ files to the same reference genome using the same version of Cell Ranger, you and your colleague should have gotten the exact same value for mean reads per cell. It's possible that your colleague used a newer version that counted intronic reads by default.

I'd recommend reaching out to support@10xgenomics.com who can help you with this question.