0
$\begingroup$

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?

$\endgroup$
0
3
$\begingroup$

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

$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service, privacy policy and cookie policy

Not the answer you're looking for? Browse other questions tagged or ask your own question.