CD45R isoforms in RNA-seq
Hello!
I am classifying cells using human scRNA-seq data processed through cellranger, and I realize that my cleaned data only has expression information to the level of CD45R/PTPRC and does not have information on CD45R isoforms CD45RA and CD45RO which are useful for differentiating immune cell types. I do not believe that these isoforms are differentiated in the reference genome I used since they don't have different gene symbols.
Does anyone have experience with differentiating the two in RNA-seq? Would this require creating a custom reference genome?
Thanks!
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dioscorea.bulbifera •
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See this paper where those isoforms were resolved:
https://www.nature.com/articles/s41592-018-0303-9
A reference transcriptome might be more useful for your purposes (i.e. isoform-level analysis).
I may be misinterpreting the comment, but where would I find a reference transcriptome that includes gene isoforms?