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Old 03-12-2019, 06:56 AM   #1
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Location: UK

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Default ATAC-seq library sequencing


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":

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.
OlgaMikh is offline   Reply With Quote
Old 03-12-2019, 01:19 PM   #2
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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.
luc is offline   Reply With Quote

atac-seq, depth, illumina, pooling samples

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