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Old 02-26-2013, 12:39 AM   #1
not just another member
Location: Belgium

Join Date: Aug 2010
Posts: 264
Default 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 ?


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