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?
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...10-14-2026, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...