I am planning my first RNA-Seq experiment and wanted to make sure I was on the right track. I am going to be sequencing the transcriptome of 700 human lymphocyte samples on the Illumina HiSeq 2000 to look at expression differences, alternative splicing, and SNPs.
After looking through numerous papers, it doesn't seem like there is a clear consensus on the level of coverage needed. It seems like the majority of papers recommend a minimum of 30X coverage. Does anyone have any input on going lower or higher than 30X coverage?
Thanks for your help!
After looking through numerous papers, it doesn't seem like there is a clear consensus on the level of coverage needed. It seems like the majority of papers recommend a minimum of 30X coverage. Does anyone have any input on going lower or higher than 30X coverage?
Thanks for your help!
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