Compare different library

Question

[inminin]

Hello,

I have total RNA sequencing data (treatment 4, control 5), but we used different library sequencing for one treatment sample.

Can I do DESeq2 analysis with considering a batch effect for one sample?

sample treatment batch
s1 control A
s2 control A
s3 control A
s4 control A
s5 control A
s6 treatment A
s7 treatment A
s8 treatment A
s9 treatment A
s10 treatment B



dds <- DESeqDataSetFromMatrix(countData = countData,colData = colData,design = ~ batch + treatment)
dds$treatment <- factor(dds$treatment, levels=c("control", "treatment"))
dds$batch <- factor(dds$batch, levels=c("A", "B"))
dds <- DESeq(dds, full=design(dds), reduced = ~ batch)

Thanks,

[WouterDeCoster]

In general, no, you cannot compare samples with different conditions in library prep.
RNA-direct? Like nanopore direct RNA-sequencing?

[Mark]

I agree with Wouter. You can but your results will be widely inaccurate because of all the compounding factors that arise when different sequencing methods are used. Can you repeat the controls using the same method as the treatment groups?

[inminin]

Thanks for your reply, I'll consider changing my method.

[WouterDeCoster]

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