I apologize if this question has already been asked, but I couldn't find the exact info I was looking for, so I decided to just ask my specific question directly.
I'm trying to set up a run on a GAIIx with 16 samples using 2 lanes, so 8 samples in each lane. We're doing targeted sequencing (not whole exome) and there are a total of 922,000 amplicon bases in the complete design (560,000 unique loci bases). We're trying to get 30X coverage, 20X coverage at a minimum. We're doing a run length of 72bp and we're thinking of doing single read.
What I'm trying to figure out:
Is single read going to provide enough coverage of these samples or should we do a paired-end run? (We're sharing a flowcell with another group and they're doing single read)
How do I figure out how many reads I need to get 30X coverage of 8 samples per lane?
I hope I'm asking my questions right and providing the right info. This is the first time I'm figuring this out by myself so I just want to make sure I'm loading enough of each sample, and whether I'm going to get enough coverage on single read.
Thanks so much for your help!
I'm trying to set up a run on a GAIIx with 16 samples using 2 lanes, so 8 samples in each lane. We're doing targeted sequencing (not whole exome) and there are a total of 922,000 amplicon bases in the complete design (560,000 unique loci bases). We're trying to get 30X coverage, 20X coverage at a minimum. We're doing a run length of 72bp and we're thinking of doing single read.
What I'm trying to figure out:
Is single read going to provide enough coverage of these samples or should we do a paired-end run? (We're sharing a flowcell with another group and they're doing single read)
How do I figure out how many reads I need to get 30X coverage of 8 samples per lane?
I hope I'm asking my questions right and providing the right info. This is the first time I'm figuring this out by myself so I just want to make sure I'm loading enough of each sample, and whether I'm going to get enough coverage on single read.
Thanks so much for your help!
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