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

Join Date: Apr 2013
Posts: 57
Lightbulb ChIPSeq sequencing depth for histone modifications

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!
priya is offline   Reply With Quote
Old 01-24-2019, 01:01 PM   #2
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?
atpoint is offline   Reply With Quote

chip-seq, chip-seq analysis, histone modifications, illumina hiseq

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