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FredHutch / Galeano-Nino-Bullman-Intratumoral-Microbiota_2022

Analysis code used in Galeano Nino et al., Impact of Intratumoral Microbiota on Spatial and Cellular Heterogeneity in human cancer. 2022
MIT License
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Visium fastqs clarification #20

Closed trus-uic closed 6 months ago

trus-uic commented 6 months ago

Hello,

Thank you for your contribution and sharing this publication data. I wanted to ask about the OSCC2 Visium data available. Are the fastqs on SRA and AWS from a Visium run to a human transcriptome probe-set?

Extended figure A indicates you mapped against the human transcriptome, then unmapped reads were processed through GATK against microbial databases. Is it the case that the provided fastqs for the Visium runs are subsets of the microbial reads?

I am asking because running these samples through spaceranger with the human probe-set provided low-to-no reads with the QC metrics indicating:

"Low Fraction of Reads Mapped Confidently to the Probe Set | 0.0% | Ideal > 50%. This can indicate use of the wrong probe set, the use of FASTQs from a poly-A based assay, or low aggregate expression. Performance may be affected."

Thank you for taking your time to clarify this and again, thank you for sharing this exciting work!

trus-uic commented 6 months ago

Confirmed this an OCT run, not FFPE which answers the question as probe-set is not relevant here. Thanks!