RNA-seq sequencing depth

NicoBxl · 02-26-2013, 12:39 AM

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 · 02-26-2013, 03:39 AM

A good place to start

http://encodeproject.org/ENCODE/prot...dards_V1.0.pdf

woodydon · 02-18-2014, 06:56 PM

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

Woody

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?

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
how to calculate the mean sequencing depth of RNA-seq	wangli	RNA Sequencing	3	02-19-2014 05:44 PM
How does read length affect sequencing depth for paired end RNA-Seq?	bob-loblaw	RNA Sequencing	2	02-15-2013 04:02 PM
Small RNA sequencing depth comparison to array or qPCR	seqfan2011	RNA Sequencing	0	05-03-2012 09:08 AM
RNA-Seq: Differential expression in RNA-seq: A matter of depth.	Newsbot!	Literature Watch	0	09-10-2011 03:12 AM

02-26-2013, 12:39 AM	#1
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	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 ? Thanks, N.

02-26-2013, 03:39 AM	#2
TonyBrooks Senior Member Location: London Join Date: Jun 2009 Posts: 298	A good place to start http://encodeproject.org/ENCODE/prot...dards_V1.0.pdf

02-18-2014, 06:56 PM	#3
woodydon Member Location: https://www.researchgate.net/profile/Woody_Lin Join Date: Jan 2010 Posts: 52	50 bp is not enough. You should try 200bp or longer. Woody

02-18-2014, 11:40 PM	#4
NicoBxl not just another member Location: Belgium Join Date: Aug 2010 Posts: 264	Hi guys, I did 2x100 finally, and it worked pretty well

02-19-2014, 03:48 PM	#5
puggie Member Location: Europe Join Date: Nov 2011 Posts: 52	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?