Does adding reads cause batch effects?
0
2
Entering edit mode
12 months ago
bioinfo ▴ 150

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

kallisto RNAseq • 845 views
ADD COMMENT
1
Entering edit mode

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

ADD REPLY
1
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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.

ADD REPLY

Login before adding your answer.

Traffic: 2990 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6