Genome Browser for Visualizing Coverage Data, Custom Annotations, and Genome Sequence?
I am looking for a genome browser that can do the following:
- Visualize coverage data, ideally by importing a bigwig file or similar
- Add a set of custom annotations to the genome by importing a bed file or similar
- Display the genome sequence with the track. Ideally be able to search the genome for a given sequence
I’m visualizing transcription factor ChIP-seq data and have identified peak locations computationally. I used the peaks to identify a sequence motif. Now I want to visualize how the coverage data is oriented around the sequence motif while including the computationally-derived peak location as an annotation.
Does anyone know of any tools that can do this well? Most genome browsers I find can do two of the three things or make it hard to identify the motif within the genome sequence.
Thank you!
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Have a look at the ucsc "hub" documentation. https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html
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Hi! You can do this on the Ensembl browser. You can find information on how to add custom data in this documentation page.