Hi,
I am working with ChIP-seq data with enrichment close to background. Only sample for the histone mark H3K4me3 look fine with well defined peaks. The others samples (H3K9me3/ac) are really bad (similar to input) and have a high rate of duplicates reads (up to 75% for the input).
To what I understand I should have a lower duplicate rates for the input samples as it should be of high diversity, but it is not the case.
I started with 10ng of DNA using the Illumina Truseq ChIP protocol as indicated with the size selection on gel.
The enrichment from ChIP-qPCR was ok, then I am wondering if something could have been wrong during the library prep (particularly to explain to high duplicates rate in the input).
Thanks
I am working with ChIP-seq data with enrichment close to background. Only sample for the histone mark H3K4me3 look fine with well defined peaks. The others samples (H3K9me3/ac) are really bad (similar to input) and have a high rate of duplicates reads (up to 75% for the input).
To what I understand I should have a lower duplicate rates for the input samples as it should be of high diversity, but it is not the case.
I started with 10ng of DNA using the Illumina Truseq ChIP protocol as indicated with the size selection on gel.
The enrichment from ChIP-qPCR was ok, then I am wondering if something could have been wrong during the library prep (particularly to explain to high duplicates rate in the input).
Thanks
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