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gene numbers after tximport summarizeToGene

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 !

rna-seq
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written by dew • dew

1 answer

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

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written by jared.andrews07 jared.andrews07

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

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written by dew • dew

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