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Old 08-31-2011, 03:44 PM   #1
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Default How to count Paired-End reads for RNA-Seq read counts

I saw a great question on the "RNA-seq Blog" (not mine)

"What sequencing depth is required for gene expression analysis? (i.e. Human sample, paired-end mappable reads, > 30 NT)"

30M was the most popular choice (for PE reads), which leads to my question.

When doing Paired-End for RNA-seq and you are targeting 30M reads, do you treat read1 and read2 together for the read count (same transcript) or separately? My thought is if the read is only to ID the transcript for counting, 15M x 15M for PE would equal 15M reads if done SR.

i.e. 30M reads could be 15M x 15M but also interpreted as 30M x 30M. Is it safe to assume 30M = 30M x 30M for PE RNA-seq?
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