RNA-seq sequencing depth

[NicoBxl]

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 ?

Thanks,

N.

[TonyBrooks]

A good place to start

http://encodeproject.org/ENCODE/protocols/dataStandards/ENCODE_RNAseq_Standards_V1.0.pdf

[woodydon]

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

Woody

[NicoBxl]

Hi guys,

I did 2x100 finally, and it worked pretty well

[puggie]

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?