<p>It's safer to import everything.  You'll want all the data for normalization and dispersion estimates.</p>

CC BY-SA 4.0
2021-02-16T18:58:17.633Z
2021-02-16T18:58:17.633Z
swbarnes2
<p>I want to check the differential expression of a specific class of transcripts (say, long non-coding RNAs) using DESeq2. Now, I know that the normalization step takes into account the total number of reads per sample. If I only input a subset of all the transcripts, the sequencing depth will change.</p>
<p>So my question is: can I simply input the subset of interest? Or should I input all transcripts, and subset the results later?</p>

<deseq2><normalization><subset>
Differential expression analysis for a subset of transcripts
# Differential expression analysis for a subset of transcripts

(Asked by: username_0 on 2021-02-16)

I want to check the differential expression of a specific class of transcripts (say, long non-coding RNAs) using DESeq2. Now, I know that the normalization step takes into account the total number of reads per sample. If I only input a subset of all the transcripts, the sequencing depth will change.

So my question is: can I simply input the subset of interest? Or should I input all transcripts, and subset the results later?

**Tags:** deseq2, normalization, subset

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## 1 answers

### Answer by username_1 on 2021-02-16. Score: 3 | Accepted answer

It's safer to import everything. You'll want all the data for normalization and dispersion estimates.


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