I want to know how reliable, cost efficient and accurate is the data generated in MinION for studies involving transcriptomics. If you have used it, shed some light on the error rate, estimated running cost per sample, and other parameters that might affect the results of my study. Any improvements over the years till now?
Hi, we have used it and it is very cost effective. The quality is far form the quality of PacBio, however, if the genome is known, then you can easily map the Minion reads and it is enough for transcript annotation. We could identify enormous number of novel transcripts/transcript isoforms in various viruses. The yield is very high, 6-8million reads/run from this summer. Last year we obtained about 2million reads/run, so the method has improved a lot (new version of the Albacore software, new reagenst, new protocols etc are available).
Here you can read our recent publications related to MinION:
Article Transcriptome-wide survey of pseudorabies virus using next- ...
Article Dual Platform Long-Read RNA-Sequencing Dataset of the Human ...
Article Multi-Platform Sequencing Approach Reveals a Novel Transcrip...
Article Lytic Transcriptome Dataset of Varicella Zoster Virus Genera...
https://www.biorxiv.org/content/early/2018/08/23/399048
Hi, we have used it and it is very cost effective. The quality is far form the quality of PacBio, however, if the genome is known, then you can easily map the Minion reads and it is enough for transcript annotation. We could identify enormous number of novel transcripts/transcript isoforms in various viruses. The yield is very high, 6-8million reads/run from this summer. Last year we obtained about 2million reads/run, so the method has improved a lot (new version of the Albacore software, new reagenst, new protocols etc are available).
Here you can read our recent publications related to MinION:
Article Transcriptome-wide survey of pseudorabies virus using next- ...
Article Dual Platform Long-Read RNA-Sequencing Dataset of the Human ...
Article Multi-Platform Sequencing Approach Reveals a Novel Transcrip...
Article Lytic Transcriptome Dataset of Varicella Zoster Virus Genera...
https://www.biorxiv.org/content/early/2018/08/23/399048
MinION is no doubt much cost effective and cheaper overall or on per sample basis. It is reliable enough if we consider slight higher error rate than pacbio which is overcome by the cheap (cost) and huge amount of data generated per run. On the other hand, pacbio is no good if compared in data quality (minutely better), but the data generated is less at a high cost. It has a error which makes a lot of data nonsense, and has to be discarded in the end. Illumina stands firm in between both and consistent in everything - cost, reliability/quality and data generated.
Thank you Drs. Dóra Tombácz and Abhijeet Singh . Is the flow cell reusable? If yes, how many samples can be run in a single flow cell? If not, how far can barcoding help in processing multiple samples in a single run?
https://www.researchgate.net/post/Are_nanopore_flow_cells_reusable
There are some kits available to wash the flow cell, which gives the possibility of reuse. Nevertheless, the death of the pores will result in the low data generated and might also cause increased error rate. Rest answer can be seen in the link attached.
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