Sequencing depth of TCGA RNA-Seq data

woodydon · 02-18-2014, 06:36 PM

Greetings,

Does anyone know the number of reads per sample in TCGA RNA-Seq data? Any cancer type will do. Approximate 20 million reads per sample?

Woody

GenoMax · 02-19-2014, 01:10 PM

TCGA RNA-seq data (submitted by UNC) sequenced on HiSeq typically has between 60M - 150M reads per sample.

woodydon · 02-19-2014, 10:35 PM

Hi GenoMax,

Thanks for the reply. Did you mean 60M to 150M pair-end reads per samples? I assume that most of the TCGA samples don't have this much sequencing depth because some of samples were sequenced before HiSeq became popular. But, I might be out-dated with the information. If most of the TCGA samples have 60M to 150M pair-end reads, that would be nice.

Sincerely,
Woody

GenoMax · 02-20-2014, 05:07 AM

The read number is reflective of the way Illumina counts reads (30M clusters = 60M PE Reads) and is only for samples sequenced on HiSeq.

woodydon · 03-13-2014, 06:38 PM

Hi GenoMax,

Thanks for the reply. In other words, that's equal to 30M to 75M "read pairs". Am I right?

Bests,
Woody

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02-18-2014, 06:36 PM	#1
woodydon Member Location: https://www.researchgate.net/profile/Woody_Lin Join Date: Jan 2010 Posts: 52	Sequencing depth of TCGA RNA-Seq data Greetings, Does anyone know the number of reads per sample in TCGA RNA-Seq data? Any cancer type will do. Approximate 20 million reads per sample? Woody

02-19-2014, 01:10 PM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,089	TCGA RNA-seq data (submitted by UNC) sequenced on HiSeq typically has between 60M - 150M reads per sample. Last edited by GenoMax; 02-19-2014 at 01:13 PM.

02-19-2014, 10:35 PM	#3
woodydon Member Location: https://www.researchgate.net/profile/Woody_Lin Join Date: Jan 2010 Posts: 52	Hi GenoMax, Thanks for the reply. Did you mean 60M to 150M pair-end reads per samples? I assume that most of the TCGA samples don't have this much sequencing depth because some of samples were sequenced before HiSeq became popular. But, I might be out-dated with the information. If most of the TCGA samples have 60M to 150M pair-end reads, that would be nice. Sincerely, Woody

02-20-2014, 05:07 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,089	The read number is reflective of the way Illumina counts reads (30M clusters = 60M PE Reads) and is only for samples sequenced on HiSeq.

03-13-2014, 06:38 PM	#5
woodydon Member Location: https://www.researchgate.net/profile/Woody_Lin Join Date: Jan 2010 Posts: 52	Hi GenoMax, Thanks for the reply. In other words, that's equal to 30M to 75M "read pairs". Am I right? Bests, Woody