Is there a program to average read counts from technical replicates?
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22 months ago

I have cell lines where RNA was extracted and was split across two lanes giving me two technical replicates per sample. I have my read counts for each technical replicate and I am going to use edgeR to get a DEG list. Is there a program which will average the reads from the technical replicates? Thank you.

RNA-Seq edgeR • 612 views
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22 months ago

so it's the same biological sample but just run on two different lanes (where the combinations is your requested #reads) ? If so, simply concatenate the two technical repeats into a single file and work with that one.

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Yes same biological sample, wouldn't averaging be more appropriate? Concatenating the two technical seems to be a lot easier.

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You don't have to do anything manually, if you tell edgeR which samples represent the same underlying biological sample in the design matrix, you should be set.

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Thank you. I will try that!

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on top of what Friederike said, no, no need for averaging. That sample could just have well be run in a single lane, summing both will be enough (especially when each lane only contributes 1/2 of the amount of sequence you ordered)

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That makes sense, thank you. I will sum the reads in that case.