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Old 09-23-2013, 02:36 PM   #1
Location: tx

Join Date: Dec 2009
Posts: 46
Default RNASeq experimental design


Hope I can pick your collective wisdom/experience.

A collaborator is planning to carry out an RNASeq experiment and separately, a RIPSeq experiment, and is looking for guidance regarding reads required for both. The genome size is ~ 112.3 MB, and they are planning to use Illumina platform.

How to calculate the number of reads required?

What is the fold coverage required for accurate gene expression values?

How many samples per lane to achieve the # reads required?

Better to get paired-end or is single read OK

Re: read length - as long as you can afford? or will shorter reads be OK

Any and all advice welcomed

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