ChIPSeq sequencing depth for histone modifications

priya · 01-23-2019, 01:20 AM

Hi,
We would like to sequence mouse Histone modification (H3K4me3,H3K4me1,H3K27me3,H3K27ac) chip-seq samples using illumina Hiseq2500. Previously we sequenced to depth of 40M reads/sample. And the number of enriched sites were good enough. Now, we would like to minimize the depth to 20M reads/sample. Is this sequencing depth (20Mreads) sufficient enough to analyze histone modification sites?
Looking forward for your inputs!

Thank you!

atpoint · 01-24-2019, 02:01 PM

Why don't you subsample your existing data to 20mio reads and see if the results are good enough for what you want to do with them?

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01-23-2019, 01:20 AM	#1
priya Member Location: sweden Join Date: Apr 2013 Posts: 57	ChIPSeq sequencing depth for histone modifications Hi, We would like to sequence mouse Histone modification (H3K4me3,H3K4me1,H3K27me3,H3K27ac) chip-seq samples using illumina Hiseq2500. Previously we sequenced to depth of 40M reads/sample. And the number of enriched sites were good enough. Now, we would like to minimize the depth to 20M reads/sample. Is this sequencing depth (20Mreads) sufficient enough to analyze histone modification sites? Looking forward for your inputs! Thank you!

01-24-2019, 02:01 PM	#2
atpoint Member Location: Muenster Join Date: Apr 2016 Posts: 14	Why don't you subsample your existing data to 20mio reads and see if the results are good enough for what you want to do with them?