INC1877237 Resolved --> Filtering .bed Track file

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05-12-2026 07:00 PM PDT - Angela Rossi-Steele ^Comments

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03-13-2024 11:37 AM PDT - Guest ^Comments

reply from: matte...@unibe.ch
Dear all,

I would like to manage/understand how to go to our gene loci of interest and filter the field Name of item.

Using this chromHMM track (https://genome.ucsc.edu/cgi-bin/hgTables?db=mm10&hgta_group=regulation&hgta_track=encode3RenChromHmm&hgta_table=encode3RenChromHmmHeartE11&hgta_doSchema=describe+table+schema)

I could select the loci and create a track activating the Name of item filtering option, this to further visualize only 2 items in the track - such as :

* State 6 - Bright Yellow - Enhancer, Strong TSS-proximal (En-Sp)
* State 7 - Light Yellow - Enhancer, Weak (En-W)
Kind regards,
Zoia Matteo


Matteo Zoia, Ph.D. Student
Gene Regulation & Cardiac Development
Osterwalder Lab
Department for BioMedical Research (DBMR)
University of Bern
Murtenstrasse 28, 369
CH - 3008 Bern
SWITZERLAND

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03-13-2024 10:24 AM PDT - Tristan Carkeet ^Comments

Hi Matteo, we need a little more clarity to see if we can help you with this.

Are you referencing the UCSC Genome Browser in your research/manuscript?

If not, can you be more specific on the exact resource you are trying to use or reference?

 

Information you provided

Requested For: matte...@unibe.ch

Filtering .bed Track file

User Name:Matteo Zoia
Email: matte...@unibe.ch
Phone Number: 0041794421765

Description : I don't manage to filter multiple names at the same time in the the 4th column of a .bed Track. Is it possible?

 

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Tech view: INC1877237

 

Ref:MSG12508067

[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

To filter the ENCODE track to visualize only states 6 and 7, the best way is to create a custom track using the Table Browser. A link to quickly select the track in the Table Browser is on the schema page you shared.

https://genome.ucsc.edu/cgi-bin/hgTables?db=mm10&hgta_group=regulation&hgta_track=encode3RenChromHmm&hgta_table=encode3RenChromHmmHeartE11&hgta_doSchema=describe+table+schema

1. Go to Table Browser (Tools > Table Browser)
2. Select your track (encode3RenChromHmm)
3. Choose your specific table (encode3RenChromHmmHeartE11)
4. Click "filter" button
5. Set filter: "name does match" and enter: `En-Sp | En-W` (using regex pattern)
6. Click "submit" to apply filter
7. Choose output format as "Custom Track" and get output

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 to genom...@soe.ucsc.edu instead.

Jairo Navarro
UCSC Genome Browser

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