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I have a few hundred SE50 samples from the old days. The rest are all by PE150. To combine them, I converted PE150 to SE50 by taking only R1 and trimming down to 50 bases. Are the products the same as the real SE50? My data analyst told me that she still saw batch effects. I am confused.
SE50 samples were all sequenced on Hiseq4000. Only a few batches of PE150 were done on Hiseq4000 while the rest were on Novaseq plaforms. Do these two platforms cause noticeable batch effects?
SE50 samples were all sequenced on Hiseq4000. Only a few batches of PE150 were done on Hiseq4000 while the rest were on Novaseq plaforms. Do these two platforms cause noticeable batch effects?