Read count track for Tabula Muris dataset

[Manjegowda, Mohan C (mcm3ha)]

Hello,

I found the reads mapping to MCU gene beginning do not match with the RefSeq coordinates. I was wondering if this is a technical issue and if this affects the expression level measurement. Because, although the expression level is very high in the microglia compared to other cell types (attached figure), the median expression level per cell is not very different from macrophage. Moreover, % cells with >0 counts are more in macrophages (attached figure). I would like to know if this is of any concern.

Please let me know if you need any further details.

Thanks,

Mohan

Mohan C Manjegowda, PhD

Senior Scientist (Desai Lab)
Dept. of Pharmacology
University of Virginia
Charlottesville, VA-22908

[Luis Nassar]

Hello, Mohan.

Thank you for your interest in the Browser.

While we can confirm that what you are pointing out here is peculiar and that the data as we display it is correct, we recommend you contact Tabula Muris directly to hear if they have a better explanation of what is occurring.

As you share, we see peaks outside the exon boundaries (https://genome.ucsc.edu/s/Lou/RM30509.1). One of our engineers points out that according to the Tabula Muris paper they used STAR aligner, which uses exon information but does not align to just exons. You could try contacting Angela Pisco (angela...@czbiohub.org) who is listed as one of the contacts for the project (https://data.humancellatlas.org/explore/projects/e0009214-c0a0-4a7b-96e2-d6a83e966ce0). If you do decide to contact them, consider cc'ing my colleague Max (mhae...@ucsc.edu) as he brought this data into the Browser and is interested to see what they have to say.

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Lou Nassar
UCSC Genomics Institute

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