I'm gearing up to do an RNA-seq experiment using the Illumina platform to identify differentially expressed transcripts in liver RNA samples from a mouse study. The output would be a minimum 30 million read depth and paired end sequences (i.e. from both ends of each transcript). I'm trying to determine if 2x75 bp reads is worth the extra cost, or if 2x50 bp sequences (i.e. 100 bp total per RNA) would be sufficient to align and identify unique transcripts. I'd appreciate any advice or experience.

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