Custom tracks on UCSC Genome Browser with a way to control items displayed by upper and lower cutoff

Question

[Ram]

Hi,

I'm trying to represent a custom file on the UCSC Genome Browser. This file contains results from a variant allele frequency comparison pipeline. Each entry has a score and a rank, and I would like to enable filtering the variants displayed by rank, by providing upper and lower thresholds.

I am not sure if this can be done with the BED format. Any pointers on how I should start looking at this problem would be really appreciated please.

Thank you.

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Ram

Answer 1

[Alex Reynolds]

You can place lower thresholds on the display of score-column BED files, by moving the mouse pointer over the track and right-clicking over it, when highlighted. Then select "Configure User Track" to apply a lower score threshold.

I don't know of a way to apply an upper bound, but that isn't to say it can't be done. That said, maybe you can bin the score ranges of your elements so that you can still use the lower-bound threshold to control their display.

This might be a good question for the UCSC Genome Browser mailing list, actually.