gene numbers after tximport summarizeToGene

Question

[dew]

Dear all,

Do you think it's correct if the gene numbers is near 40,000 after using tximport function summarizeToGene, which the first few rows look like below:

ENSG00000000003 1240.2530 1202.8513 1104.731 
ENSG00000000005    0.0000    0.0000    0.000  
ENSG00000000419 2765.0000 2541.0000 2311.000
ENSG00000000457  762.8118  644.3759  670.465  
ENSG00000000460 1101.1205 1375.5160 1057.038  
ENSG00000000938    9.0000    6.0000    7.000  

Thanks a lot !

Answer 1

[jared.andrews07]

Depends on the annotation you use, but yeah, 40k isn't surprising. I get ~55k using salmon quantifications and Gencode v19 annotations.

[dew]

Thanks a lot for your sharing! I guess it's ok, using hsapiens_gene_ensembl dataset from biomaRt, thank you!