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Old 07-05-2014, 07:58 AM   #1
Location: Japan

Join Date: Oct 2010
Posts: 52
Question Oxford Nanopore MAP: quantitative transcriptomics?

I have the option to join the Oxford Nanopore MAP. What I want to do is use MinION for (quantitative) transcriptomics, i.e. I want to reverse transcribe RNA to DNA and then sequence on MinION. This is on mouse.

Does this make any sense with respect to the capabilities of MinION?

I can't find anything on number of reads, sequencing depth... the documents I have read so far all seem to assume that I want to do genome (re-)sequencing, where - as I understand - depth is less important than length.

So can I do transcriptomics on MinION? Will I get anything except the most highly expressed genes and ribosomal RNA? Does the sequencing depth somehow depend on runtime? Also how does the speed of sequencing (bases per second) affect things?

I understand that there is not much info on MinION out there yet and the point of the MAP is probably to generate experience on this, but I would be happy if I could get ANY info on performance before I decide to join the MAP. Thanks.

tl;dr: Can I do transcriptome sequencing on MinION?
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