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  • How do I analyze repeats in my ChIP-seq data?

    I want to look for repeats enriched in my mouse ChIP-seq data. One way is to intersect peaks with the RepeatMasker track from the UCSC Genome Browser, and I've done that (downloaded using Table Browser, intersected with Bedtools). Two things I'm wondering about:

    1. The RepeatMasker track has satellite repeats but doesn't seem to differentiate between major and minor, how can I check those?

    2. I see in some papers that people align their reads to RepBase so that you can check all your reads (including those that don't align to your reference genome eg. because they are too repetitive). I made an account and downloaded RepBase19.01.fasta.tar.gz but I'm not sure which files to use. For example, I opened mousub.ref which I assume is mouse repeats and it only had 6 sequences in it. Which files should I use from RepBase to get a list of all mouse repeats, so that I can then align to them?

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