What causes very low read mapping? CUT&RUN with Bowtie2
Generally, what causes low read mapping efficiency? Some samples have 70% and others are 8-20%. I am experienced with bowtie2 and tested with/without trimming. These are human and mouse cut&run.
We are not confident in the antibodies used, but I thought bad antibodies would lead to no peaks later on rather than low alignment.
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smurph50 •
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smurph50 •
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pretty much, yes. contamination in the lab in terms of fungi or bacteria are rare in my experience. blast will just by chance give some random hits to any bacteria but chance these really were in your tube are almost zero. with these chip-like libraries and poor antibodies a failed ip is almost always the best explanation.
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No magic bullet here. Get representative reads that do not map and investigate with BLAST. You may have some unexpected contamination.