how many reads are good for detect differential expression of lncRNA

[inankai]

I am going to detect the lncRNA differential expression after certain treatment.
With RNA-Seq, how many reads is necessary for a robust analysis?
30M? 50M?

Any help is highly appreciated.

[MicheleB]

Hi Inankai,

We looked at this question in our paper in Bioinformatics:

http://bioinformatics.oxfordjournals.org/content/29/5/656

The short answer is that it depends on how efficient you sequencing protocol is, how small a fold change you want to be able to detect, and how interested you are in linc RNAs that are expressed in low quantities. For most experiments it is (theoretically) more beneficial to use extra reads to add more biological replicates than to sequence existing replicates more deeply.

We did not look specifically at linc RNAs but if you have pilot data or can use an available data set with replicates to look at linc RNA you can run a power analysis through our server here:

http://euler.bc.edu/marthlab/scotty/scotty.php

That should show you what happens when you sequence more deeply or add more reps.

If you have trouble or questions my email is on the help site.

Michele