Dear all,
I know that this thread was already asked before, however I wonder if someone has a new/better explanation/suggestions.
I am encountering a high duplication level in my chip-seq libraries. almost 99% of the reads are eliminated when considering only one read to map with Bowtie.
I am starting my libraries with around 2/3 ng of IP materials. I am using the NEB kit for the library prep. The library concentration is not that high too.
I am doing 18 cycles. I am multiplexing 10 samples at a time.
Inputs sequencing seems better with around 40% of duplication.
Any suggestion is the most welcome,
Best,
I know that this thread was already asked before, however I wonder if someone has a new/better explanation/suggestions.
I am encountering a high duplication level in my chip-seq libraries. almost 99% of the reads are eliminated when considering only one read to map with Bowtie.
I am starting my libraries with around 2/3 ng of IP materials. I am using the NEB kit for the library prep. The library concentration is not that high too.
I am doing 18 cycles. I am multiplexing 10 samples at a time.
Inputs sequencing seems better with around 40% of duplication.
Any suggestion is the most welcome,
Best,
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