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GoekeLab / sg-nex-data

Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
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Number of PCR cycles #8

Closed callumparr closed 3 years ago

callumparr commented 3 years ago

I went through the Biorxiv print, particularly the methods and supplementary tables but I could not see any info on the number of PCR cycles used.

It seems there quite bit of PCR bias when comparing genes between cDNA and cDNA-PCR. Was. this is no. of cycle-dependent or is more to do with the alignment of genes with repetitive elements?

jonathangoeke commented 3 years ago

Hi @callumparr I assume this is related to PCR amplification, but we used the standard PCR protocol so the cycle number is the same I believe

callumparr commented 3 years ago

Ah yes was the PCR cycle number I was enquiring about. I looked up the nanopore protocol and says 10-18 cycles but in their own data, they did not go much into bias and then they did not see much up to 10 cycles I think. But from your data, it also seems to be an issue of repetitive elements not so much cycle number that causes large bias when comparing PCR-free and PCR methods.