Hi all,
I am about to undertake a study investigating the gene expression differences between human twins using tissue from the pregnancy. I aim to quantify expression differences and hopefully allele-specific differences and splice variants between the individuals.
The abundance of transcripts differentially expressed is largely unknown and I was hoping for some input on calculating what sequencing depth I should be aiming for.
From trolling the literature I figure 8 gigabases of data per sample from 100bp paired-end Illumina Hi-seq run should give me more than enough data.
I also plan on running a 35bp single end library in addition to this for each sample for miRNA, etc.
Any thoughts, comments etc on how deep I should aim with the human transcriptome?
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