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Old 02-18-2014, 06:36 PM   #1
woodydon
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Default 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
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Old 02-19-2014, 01:10 PM   #2
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TCGA RNA-seq data (submitted by UNC) sequenced on HiSeq typically has between 60M - 150M reads per sample.

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Old 02-19-2014, 10:35 PM   #3
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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
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Old 02-20-2014, 05:07 AM   #4
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The read number is reflective of the way Illumina counts reads (30M clusters = 60M PE Reads) and is only for samples sequenced on HiSeq.
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Old 03-13-2014, 06:38 PM   #5
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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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