question about read depth for splice variant detection
Dear All,
I plan to perform RNA-seq recently, but I am a newer to RNA-seq and I found it was hard to determine the read length and sequencing depth(read numbers per sample).
I use human cell lines and I want to detect alternative splice variants as well as differential gene expression, I will perform RNA seq using illumina 2000/2500.
So my question is how many read length and read number should I choose?
It looks the read numbers is the more the better for AS, but due to our limit budget, I want to find a cost effective way but can still generate a good result.
The core in our university recommend me run 1 sample per lane, so the price will be too high to be acceptable. Do I really need that read depth?
I saw some people suggested >100M pair-end for splice variants detection, that means 100M reads or 100M paired-reads? I was confused.
Right now, I plan to use paired-end 2x69, run 3 samples per lane on illumina Highseq 2500 RAPID run(about 50M paired-reads per sample), is this reasonable? I am really not sure!
Please advice me if you could, thanks!
Rui,
I plan to perform RNA-seq recently, but I am a newer to RNA-seq and I found it was hard to determine the read length and sequencing depth(read numbers per sample).
I use human cell lines and I want to detect alternative splice variants as well as differential gene expression, I will perform RNA seq using illumina 2000/2500.
So my question is how many read length and read number should I choose?
It looks the read numbers is the more the better for AS, but due to our limit budget, I want to find a cost effective way but can still generate a good result.
The core in our university recommend me run 1 sample per lane, so the price will be too high to be acceptable. Do I really need that read depth?
I saw some people suggested >100M pair-end for splice variants detection, that means 100M reads or 100M paired-reads? I was confused.
Right now, I plan to use paired-end 2x69, run 3 samples per lane on illumina Highseq 2500 RAPID run(about 50M paired-reads per sample), is this reasonable? I am really not sure!
Please advice me if you could, thanks!
Rui,