automating highlight addition in UCSC hg38 browser with custom .bed file track

[Alistair Garratt]

Dear UCSC,

I am currently using a custom .bed file as a track to highlight
particular repeat elements in the hg38 assembly. As I wish to see the
overlaps of the repeats with the ChIP-seq signals of my set of loaded
transcription factors from ENCODE, I have to stroke over manually each
individual .bed file annotation at the top and highlight these one by
one. This is laborious and not possible for the whole genome given the
fact that the .bed file has over 600 thousand entries. Is it possible to
get the browser to make vertical highlights down the browser view that
match the entries of the .bed file? Would this entail you programming a
custom browser session or could you incorporate such a functionality in
the general browser interface?

Many thanks,

Alistair

--
____________________________

Prof. Dr. Alistair N. Garratt
Institute for Cell Biology and Neurobiology
Center for Anatomy
CharitéCrossOver
Charité University Hospital
Charitéplatz 1
10117 Berlin

Tel: +49 30 2009 3004
Fax: +49 30 2009 3005
Mobile: +49 151 52549952

alistair...@alumni.charite.de

[Robert Kuhn]

Dear Alistair,

When I was on the Browser staff, I made a series of videos (3 of them) about making links to the 

Genome Browser.  The following video describes making links with highlights.  It may help you with this:

https://www.youtube.com/watch?v=xmcyz2GyRKA

The link I have marked in the summary will take you directly to the conversation about  highlighting.

best wishes,

     --b0b kuhn

Robert Kuhn, PhD

Associate Director UCSC Genome Browser (retired)

dba  Robert Kuhn Consulting

PS.  I am now working independently, still giving Genome Browser workshops.  Let me know if you are interested.

Part 2: Genome Browser links: Links inside genes and more tricks

2,117 views Jul 27, 2020

Part Two of a three-part series about making links, featuring how to fashion a URL that gets to a gene or a location within a gene using nucleotide or amino-acid numbers instead of genomic coordinates, how to set highlights and how to find variables for setting browser parameters. The third installment will show how to link to composite tracks, how to access your remotely-hosted custom tracks and how to make useful links in your spreadsheets. transcript: https://genome.ucsc.edu/training/vids... [ 1:20] The basic URL [ 2:01] Link to a coding nucleotide [ 4:53] Link to an amino acid [ 6:33] Links with gene names, not coordinates [ 7:44] Link with Short Match [ 9:12] Links with highlights <----------------------------------------------------- [13:27] Finding other options: The cart [16:01] View Browser graphic only: hgRenderTracks

--

---
You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.
To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu.
To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/437cb0f0-b3b5-4a93-875a-e2358c360212%40alumni.charite.de.

[Gerardo Perez]

Hello, Alistair.

Thank you for your interest in the Genome Browser and for sending your inquiry.

Unfortunately, we currently don’t have a feature to add vertical highlights that match the entries of a BED file. We have an internal ticket to add this as a feature and have noted your inquiry. We will assess this feature when allocating time for projects.

You might also find the Intersection option in the Table Browser useful for identifying overlaps between the repeats and your ChIP-seq data. The Intersection option combines the output of two queries into a single set of data based on specific join criteria. For example, you can upload your BED file as a custom track (https://genome.ucsc.edu/cgi-bin/hgCustom) and then run an intersection using the Table Browser. If you are unfamiliar with the Table Browser, please see the User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.

Here are some previous discussions related to using the Intersection option that you may find helpful:
https://groups.google.com/a/soe.ucsc.edu/g/genome/c/rPCvGprlxC0/m/ikhjKC-3Sv0J
https://groups.google.com/a/soe.ucsc.edu/g/genome/c/0B-Er4Szbts/m/-6rV-X2PNssJ

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

To unsubscribe from this group and stop receiving emails from it, send an email to genome-www+...@soe.ucsc.edu.