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Old 03-12-2019, 05:56 AM   #1
OlgaMikh
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Default ATAC-seq library sequencing

Hi,

I am about to submit my first mouse ATAC-seq libraries for sequencing, but I have doubts regarding the number of libraries to pool in one 100bp paired-end HiSeq2500 Rapid Run.
The Buenostro paper is suggesting >50M mapped reads per sample (in case of human genome), and the Rapid Run, according to Illumina's specifications, should yield "600 million paired end reads": https://emea.illumina.com/systems/se...fications.html

My question is: does it mean I can pool 12 samples? Or did Buenostro mean 50 million pairs, which means 100 million reads per sample -- meaning I can only pool 6 samples in one run?

Many thanks for helping to resolve this confusion.
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Old 03-12-2019, 12:19 PM   #2
luc
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Hi Olga,

your math seems correct. Six samples to sequence about 50 million library molecules each. Buenrostro et al. generally refer to paired-reads in their papers.
But you can certainly pool more libraries, analyze the data of the first lane, and then sequence additional lanes if needed.
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atac-seq, depth, illumina, pooling samples

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