Hi everyone, if I do not use spike-in RNA isoform controls for a customized RNA sequencing experiment (not the whole transcriptome, just based on few specific genes we are interesting), so is there anything we can do later on during the analysis part to cover up any technical variability inter and intra experiments apart from the existing biological variability. Can we still rely on such data? or any tools available for such case to sort it out?
Any advice, suggestions or tips????
Thanks.....
Hi Jawwad Ahmad .
What is the purpose of the experiment? Is it RNA variants? Modifications? Expression? How do you plan the selected genes of interest?
There are many ways how to tackle the variability but to tell you more we need to know the purpose of the experiment.
Spike-ins don't have to be always necessary.
May be, you will reconsider your experiment after reading this nice paper from Chen et al 2016.
Chen K, Hu Z, Xia Z, Zhao D, Li W, Tyler JK. 2016. The overlooked fact: fundamental need for spike-in control for virtually all genome-wide analyses. Mol Cell Biol 36:662–667
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