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Old 10-18-2017, 04:13 PM   #1
deanie
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Location: Australia

Join Date: Apr 2014
Posts: 2
Default Dealing with technical replicates

First question, can anyone confirm these are indeed technical replicates?

3 blood samples taken from the same individual, each processed separately and final libraries pooled for sequencing (paired-end). So have a pair of fastq files for each of the replicates.

Second question, what are your opinions on how to deal with the technical replicates during differential expression analysis?

I've heard of technical replicates sequenced over different lanes and then combining the fastqs. In this lab's experiment there is no lane variation due to the multiplexing. Is it still sensible to combine them in the case described above?

Or separately process the fastqs for each replicate (i.e. qc, trimming, counts) and then combine the read counts? Based on what I read most people sum the counts of the technical replicates, with a few posts suggesting averaging them.

TIA!
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