I will be performing an RNA-seq experiment for differential gene expression with Illumina HiSeq 2500 (100 or 150bp pair-end). My experiment is designed as 6 control conditions and 6 treatments. So with 3 biological replicates each, it gives an amount of 36 samples. I know HiSeq 2500 yields around 190-240 million reads per lane.
Now, the problem is that I don't have much idea of how many reads per sample or per condition I would be needing. Thus, I also don't know how many lanes would be necessary for these 36 samples.
I work with filamentous fungi and the aim is to evaluate whole-transcriptome changes. Maybe it has to do with the size of the target genome (the genome is already sequenced), but in which relation exactly? Can someone please help me with this?
Now, the problem is that I don't have much idea of how many reads per sample or per condition I would be needing. Thus, I also don't know how many lanes would be necessary for these 36 samples.
I work with filamentous fungi and the aim is to evaluate whole-transcriptome changes. Maybe it has to do with the size of the target genome (the genome is already sequenced), but in which relation exactly? Can someone please help me with this?
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