Sequencing depth of TCGA RNA-Seq data

[woodydon]

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]

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

[woodydon]

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]

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]

Hi GenoMax,

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

Bests,
Woody