Is there a need to include 2nd factor if there's only paired reads in the dataset for DeSeq2?

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In the tutorial it is suggested that we include a second factor “sequencing”: and include paired and unpaired count files. My question is if all my read files are paired, is there a need to do this step in DeSeq2?

GalaxyProject tutorial,

Time point: 4:01 - shows that they have both paired and unpaired reads.
24:19 - shows that they are adding a second factor

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Hi @Sanjukta_Ghosh
factors are determined by nature of your experiment. If all samples were sequenced on the same platform and groups nicely cluster together on PCA plot, you probably don’t need additional factor. Maybe check this tutorial for more information:

Kind regards,
Igor

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Hi @igor
all my samples were sequenced on the same platform but the PCA plot looks like this:
Capture

I could not get much idea from this tutorial. It could be that I missed something, if so please highlight the relevant info.

Thanks in advance.

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