Hi all,
We'd like to perform some RNA-seq to look at gene expression level changes in mouse hippocampus due to a treatment of interest to us. We're not interested in finding new transcripts or looking for differences in splice junctions or anything of that sort. Consequently, I'm curious what people are recommending these days in terms of read depth.
On a related note, I've read a number of people here suggesting that paired end reads are probably not required for our sort of project. If that's the case, I'm curious what sort of read lengths (36bp, 50bp, etc.) people having been using that give them meaningful results.
Any suggestions you might have would be appreciated.
We'd like to perform some RNA-seq to look at gene expression level changes in mouse hippocampus due to a treatment of interest to us. We're not interested in finding new transcripts or looking for differences in splice junctions or anything of that sort. Consequently, I'm curious what people are recommending these days in terms of read depth.
On a related note, I've read a number of people here suggesting that paired end reads are probably not required for our sort of project. If that's the case, I'm curious what sort of read lengths (36bp, 50bp, etc.) people having been using that give them meaningful results.
Any suggestions you might have would be appreciated.
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