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Old 08-09-2013, 12:37 PM   #1
JQL
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Default microRNA sequencing depth

Hi,

Sorry if this has already been discussed before. I wonder how many samples one can pool into one Illumina hiseq2000 lane for miR seq? I was told each lane can generate 180MM SR50 reads.

thanks in advance.
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Old 08-28-2015, 03:11 PM   #2
mbhudson
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I have been trying to figure out the same thing. Here is a good paper http://www.biomedcentral.com/1471-2164/15/423

From the paper "One of the common questions in miRNA-Seq design is how deep miRNA sequencing needs to be. To provide some guidance to investigators, we conducted a simulation study with a miRNA-Seq sample with 25 million of reads. The experiment started from the complete dataset and then randomly drew 0.5, 1, and 2 to 24 with 2 million increments. At the full data, 1,121 miRNAs were detectable with at least 2 reads and these miRNAs were binned into 5 levels of expression. Almost all miRNAs with expression greater than 15 reads (58% of expressed miRNAs) were detectable at 6–8 million of sequence reads. With 12–18 million of reads, 78% of all expressed miRNAs could be detected. Although further increase of sequence depth could capture very low expressed miRNAs, their biological significance can be questionable thus a sequence depth of at least 10 million reads per sample could get a reasonable capture for expressed miRNAs (Figure 5) assuming the miRNA-Seq library mostly consists of miRNAs."
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