We have mapped sequence data generated by 10X 3' single cell v3 kit (10X Genomics) using cell ranger. wget http://cf.10xgenomics.com/supp/cell-exp/refdata-cellranger-GRCh38-3.0.0.tar.gz

After that we made TPM matrix using TxDb.Hsapiens.UCSC.hg38.knownGene library. https://bioconductor.org/packages/release/data/annotation/html/TxDb.Hsapiens.UCSC.hg38.knownGene.html

We noticed that the vast majority of the immunoglobulin genes and red blood cell markers are missing in our dataset perhaps because such genes are not in the above annotation list in bioconductor. Would you be able to guide us with generating TPM matrix containing those genes?

Thank you.

Hi,

You would need to be a lot more specific about what you've done and maybe show some code. If at some point you've used genes() to extract the genes from TxDb.Hsapiens.UCSC.hg38.knownGene, make sure to set single.strand.genes.only to FALSE otherwise some genes could be dropped. See ?genes for more information.

H.