found genes in expression matrix that are not in the gtf, all end in .1

10XGenomics / cellranger

10x Genomics Single Cell Analysis

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found genes in expression matrix that are not in the gtf, all end in .1 #60

Closed slyahn closed 4 years ago

slyahn commented 4 years ago

Hello,

We have run a standard gene expression analysis using the refdata-cellranger-GRCh38-3.0.0 files, but I noticed that there are 18 extra genes in the expression matrix compared to the gtf, all of which end in .1

For example: IGF2.1 DIABLO.1 EMG1.1 TBCE.1

The .1 version of the gene does not share the same expression pattern as the normal gene name (IGF2.1 expression is not the same as IGF2).

What are these .1 genes?

slyahn commented 4 years ago

The reason this happens is because these genes have multiple ensembl IDs in the gtf. I'll close this issue.