What's are the advantages and disadvantages of of both the process. Which one is the best and why?
My research question is focused on observing the differential gene expression and identification of candidate genes in response to stress tolerance.
Illumina has this to say on the subject:
https://www.illumina.com/science/technology/next-generation-sequencing/paired-end-vs-single-read-sequencing.html
paired end gives better quality but it also costs more. So it will depend how you want to balance cost/budget versus quality.
Please don't quote me (!) but based on your aim of differential gene expression to find candidates, personally I feel single end is a good place to start, especially if there will be validation by other methods.
This NGS guide gives a good explanation about the difference between two types of reads:
https://genohub.com/next-generation-sequencing-guide/
For differential expression analysis, generally, 1x50 or 1x75 bp reads are sufficient.
I know this is a bit late, but if you are simply looking for differential gene expression, you are likely to be ok using single end sequencing. As with everything, you get what you pay for- paired end sequencing will always be the "better" option, but for differential expression analysis it is likely not worth the additional cost. For transcriptome profiling however (i.e. isoform and splicing differences) it seems that paired end would be better.
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