ATAC-seq library sequencing

OlgaMikh · 03-12-2019, 06:56 AM

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.

luc · 03-12-2019, 01:19 PM

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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03-12-2019, 06:56 AM	#1
OlgaMikh Junior Member Location: UK Join Date: Feb 2012 Posts: 8	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.

03-12-2019, 01:19 PM	#2
luc Senior Member Location: US Join Date: Dec 2010 Posts: 453	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.