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NicoBxl 02-26-2013 12:39 AM

RNA-seq sequencing depth
Hi everybody,

I've several questions about sequencing depth and RNA-seq. So, what is the minimal read count (in the raw data) to have a good view of :

1. gene expression ?
2. Differential splicing ?
3. Low expressed transcripts (like lncRNA) ?
4. Fusion gene ?

I read that 100M is a minimum for fusion gene ? Is that correct ?
I want to do 2x50bp strand-specific libraires and sequenced them on a HiSeq 2000. Is 50bp enough to find accurately fusion gene ?



TonyBrooks 02-26-2013 03:39 AM

A good place to start

woodydon 02-18-2014 06:56 PM

50 bp is not enough. You should try 200bp or longer.


NicoBxl 02-18-2014 11:40 PM

Hi guys,

I did 2x100 finally, and it worked pretty well ;)

puggie 02-19-2014 03:48 PM

I'm glad it work out for you :) Depending on what you are looking for depth is something to consider.

Out of curiosity how did you sequence, i.e. reads/sample?

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