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Old 01-23-2019, 12:20 AM   #1
priya
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Location: sweden

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Lightbulb 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!
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Old 01-24-2019, 01:01 PM   #2
atpoint
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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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chip-seq, chip-seq analysis, histone modifications, illumina hiseq

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