Hi, newbie to ChiP-seq. I have two libraries prepared with the Thermo Scientific Pierce Magnetic ChIP kit, micrococcal nuclease digestion and sonication. QC from an Agilent Tapestation shows several low peaks at ~180bp, 363, 537 and 713bp respectively. Normal practice I'm told is to pick at 180bp and generate libraries from that. With such a tiny peak there, I could either:
- stick with 180bp, but not have much material to generate my library from
- pick from several peaks but then end up with fragments of different sizes, which could make the bioinformatics hard.
So would I:
- do the size selection and end up with a small amount of material
- skip the size selection (or rather have a broad size selection) and deal with the consequences later
Any advice appreciated, this experiment is unlikely to be repeated so I'll need to work with what I've got.
thanks.
- stick with 180bp, but not have much material to generate my library from
- pick from several peaks but then end up with fragments of different sizes, which could make the bioinformatics hard.
So would I:
- do the size selection and end up with a small amount of material
- skip the size selection (or rather have a broad size selection) and deal with the consequences later
Any advice appreciated, this experiment is unlikely to be repeated so I'll need to work with what I've got.
thanks.
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