Do I need to correct for sequencing depth in bulk RNA seq?
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13 months ago
bioinfo ▴ 140

Hello,

I had 6 samples sequenced in a facility and most of them have similar amount of reads except for one that has twice as much. Do I need to do anything to correct for this?

I aligned with Kallisto and I was going to use either DESeq2 or EdgeR to do differential analysis. From what I understood reading at the documentation both of those packages correct for sequencing depth. Is that enough or do I need to perform any other correction?

Thank you

kallisto RNA-seq • 520 views
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I recommend doing a PCA and seeing if you see the samples are grouped as expected or not. Also, see if the highly sequenced one is separated from the others.

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13 months ago

Start your analysis and normalize as is typical. Unless it proves an outlier via PCA or such, there's no need to worry about it.

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