Whole transcriptome

Question

[a.fathi]

I need to do Human whole transcriptome using oxford Nanopore but I can't to calculate the depth of coverage on long read. in short read I need 50 millions read per sample if i need the same output but by long read how can i calculate it, consider that the reads in short read approach 150 bp while in the long read may by kb,s.. the flow cell will use is Minion

Answer 1

[GenoMax]

Not exactly sure what you are asking but in case of short reads the likelyhood of having multiple reads covering a given location is higher because of the read numbers involved. If you are using a MinION you are going to get much fewer reads (unless you are planning to run multiple cells).

You can still calculate the coverage by using one of the methods here: How to calculate coverage in short-reads and long-reads in RNA-Seq?

[a.fathi]

Thank you so much, my question was about: i need to do Human Whole transcriptome sequencing on Oxford nanopore but i cant to calculate the number of reads per sample as in NGS which is 50 million reads per sample in 150 bp read length

i will use Minion flow cell. How many of sample should be loaded on flow cell

How can calculate the depth of coverage on ONT