Question: how to find expressed genes in RNAseq
gravatar for melkile26
4 weeks ago by
melkile260 wrote:

Hello all,

I am a newbie to RNAseq analysis. I am comparing (treatment vs control). Briefly, I mapped the RNA-seq reads to the reference genome using STAR and I used featureCounts to quantify the reads mapped to the reference genes and found the gene counts. Before I start the deferentially expression analysis, I would like to find the expressed genes. I use the command below and found 15463 genes, is it right to say, out of 24321 genes 15463 genes are expressed.

dds<-dds[rowSums(counts(dds)) > 0,]

dds<-dds[rowSums(counts(dds)) > 5]

ADD COMMENTlink modified 18 days ago • written 4 weeks ago by melkile260
Answer: how to find expressed genes in RNAseq
gravatar for Michael Love
4 weeks ago by
Michael Love21k
United States
Michael Love21k wrote:

We don’t have anything in DESeq2 to define what is expressed. Sometime people would use a TPM cutoff I suppose. If you have imported with tximport then the TPM matrix will be available.

ADD COMMENTlink written 4 weeks ago by Michael Love21k

Hi Michael,

Thanks for your reply, I just learned, even in using the command below doesn't related to in filtering the expressed genes,

dds<-dds[rowSums(counts(dds)) > 5,]

According to DESeq2 vignette, "removing rows in which there are no reads or nearly no reads, we reduce the memory size of the dds data object and we increase the speed of the transformation and testing functions within DESeq2".

I have been using 'dds<-dds[rowSums(counts(dds)) > 5,]' command to find the expressed genes from raw counts.



ADD REPLYlink modified 4 weeks ago • written 4 weeks ago by melkile260

Dear Michale,

As I mentioned, I found the gene level counts using featureCounts, can I use tximport to import the gene level count matrix which I found using featurCounts. After importing, I am thinking to use TPM to find the expressed genes.


ADD REPLYlink written 28 days ago by melkile260
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