RNASeq experimental design

crh

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RNASeq experimental design

09-23-2013, 02:36 PM

All

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.

Questions:
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

Charles
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