Question: Should I use gene_id or gene_name in featureCounts for differential expression gene analysis?
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4 weeks ago by
biock0 wrote:

Hello! When I use featureCounts to quantify gene expression counts, there are two choices of attribute type in GTF annotation: gene_id and gene_name (specified by -g option). The default value is gene_id, while I found many studies use gene_name. What's the difference between the two choices for downstream differential expression analysis?

rna-seq ensembl gtf • 144 views
ADD COMMENTlink modified 4 weeks ago by jared.andrews072.3k • written 4 weeks ago by biock0
gravatar for jared.andrews07
4 weeks ago by
St. Louis, MO
jared.andrews072.3k wrote:

Depends what you're using for the differential expression analysis. Usually used for gene level summarization on data import into DESeq2 or whatever with tximport or the like. So really, it shouldn't matter, but you probably want to use gene_id since those identifiers are generally easier to map to different things.

ADD COMMENTlink written 4 weeks ago by jared.andrews072.3k
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