Tweet
I am looking for a software package, or R script for generating the coordinates for a heat map of repeat density. I have a repeat library, and a table of repeat locations (via RepeatMasker), but there is some overlap between repeats. Are there any good programs that can do this? My goal is to incorporate this into a circos plot.
-
-
If you convert your table of repeats into BED format, you can use BEDtools to count up the overlaps in bins across the genome. I created BED files tiled across the genome in whatever increments I wanted for the Circos plot, then used BEDtools to count up the BED features within each bin. Depending upon the detail you need, you can either use coverageBed or "intersectBed -c" to calculate the overlap counts per tile. BEDtools is also blazing fast.
-
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM -
With the launch of new single-cell sequencing platforms in 2026, the field stands at an exciting inflection point. This article surveys the most impactful advances in the field and discusses how they’re reshaping research in cancer, immunology, and beyond.
Introduction
Single-cell sequencing technologies have undergone remarkable advances over the past decade, transitioning from low-throughput experimental approaches to highly scalable platforms capable of...05-22-2026, 06:42 AM
Comment