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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
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