Does adding reads cause batch effects?

Question

[bioinfo]

Hello,

I had some samples sequenced however a couple of them did not get the amount of reads that I expected. Therefore, I was planning to rerun those 2 samples to add more reads and then merge them using cat before using kallisto to get the counts and then DESeq2. Would I have to correct for batch effects for those 2 samples when I run DESeq2?

Thank you

[GenoMax]

If the same libraries are being resequenced on the same kind of sequencer then there should be little to no batch effect.

[seidel]

As a curiosity, you could compare the two from each "batch" with kallisto and DESeq2 to see how different they are, and as GenoMax says, they should be even less different from each other than technical replicates.

[bioinfo]

Thank you. If I do a PCA on the counts following kallisto would that also help identify batch effects?

[ATpoint]

Yes, you would process sequencing and resequencing separately and then do a PCA. I would expect no relevant batch effect here.

[bioinfo]

Would the number of reads in each batch affect the PCA? I do notice some batch effect. For example, I have one batch where most samples have 20 million reads and one that has 5 million and they do separate on the PCA plot. However, I am wondering if this separation is significant since the axis on my PCA goes from -0.4 to 0.4 so it is pretty small.