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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This year’s Advances in Genome Biology and Technology (AGBT) General Meeting commemorated the 25th anniversary of the event at its original venue on Marco Island, Florida. While this year’s event didn’t include high-profile musical performances, the industry announcements and cutting-edge research still drew the attention of leading scientists.
The Headliner
The biggest announcement was Roche stepping back into the sequencing platform market. In the years since...03-03-2025, 01:39 PM -
The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...02-24-2025, 06:31 AM