[genome] Too many items to display message – RNA-Seq reads

[Enrique Medina-Acosta]

Dear UCSC Developer and Support Team,

I am trying to visualize in the UCSC Genome Browser RNA-Seq reads that were mapped through the Galaxy Toolkit and sent to UCSC Genome browser to the Galaxy tool.

The difficulty I have is the following:  when I have more than 1000 reads mapping to a given SNP, UCSC Browser does not display the reads above that limit. It just shows a bar indicating the position of the mapped reads (1^st and 2^nd custom tracks below the retroposed gene DGKZP1 (in pink) in the attached print screen) and a “Too many items to display in the full/pack mode”.

How can I get the Browser to exhibit all the reads?

Best regard,

Enrique

Prof. Dr. Enrique Medina-Acosta, M.Sc., PhD.
MyCVLattes - CNPq
MyResearcherID (ISI Web of Knowledge)
MyORCID

Senior Associate Professor
Unit Coordinator - Molecular Identification and Diagnostics Unit - NUDIM
Laboratory of Biotechnology, Center for Biosciences and Biotechnology
Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF
Building P4, rooms 212/228
Avenida Alberto Lamego 2000, Parque Califórnia, CEP 28013-602, Campos dos Goytacazes, RJ, Brazil.
Tel: +55 22 27397085

[Jairo Navarro Gonzalez]

Hello Enrique,

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

For performance reasons, the Genome Browser automatically condenses the track data into a shorter view mode when viewing many items. From the images you shared, it appears you are looking at a region greater than 2,000 bp, which may be causing the issue. If you want to be able to view these items in 'pack' or 'full', you will have to zoom into a smaller region. However, even after zooming in, there could be more items in the region than allowed by our maxItems trackDb setting.

https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#maxItems

We have added a feature request ticket to allow manually setting the maximum items to display before a track automatically condenses. Unfortunately, we do not have an estimated time of completion for this feature, but you can receive email updates about the UCSC Genome Browser by subscribing to our Announcements List:

• Subscribe: Email genome-annou...@soe.ucsc.edu
• Unsubscribe: Email genome-announ...@soe.ucsc.edu

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.

Jairo Navarro 
UCSC Genomics Institute

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[jp d]

can i put in a feature request that when the max number is met

the browser will display a random subset of items.

actually i could see that useful before the max number is met

thanks

jpd

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[Enrique Medina-Acosta]

Dear Jairo,

Thank you for your reply and for posting the ticket.

From this end, zooming in down to 300 bp did not help in either the pack of full modes. The browser still does not show all the items in the custom tracks with over 1000 lines. Being able to customize the maximum number of items to display via a pop-up window would be an asset.  

Best regards,

Enrique

Sent with Mailtrack

Prof. Dr. Enrique Medina-Acosta, M.Sc., PhD.
MyCVLattes - CNPq
MyResearcherID (ISI Web of Knowledge)
MyORCID

Senior Associate Professor
Unit Coordinator - Molecular Identification and Diagnostics Unit - NUDIM
Laboratory of Biotechnology, Center for Biosciences and Biotechnology
Universidade Estadual do Norte Fluminense Darcy Ribeiro - UENF
Building P4, rooms 212/228
Avenida Alberto Lamego 2000, Parque Califórnia, CEP 28013-602, Campos dos Goytacazes, RJ, Brazil.
Tel: +55 22 27397085

2017-12-13 17:10 GMT-02:00 Jairo Navarro Gonzalez <jnav...@ucsc.edu>:

Hello Enrique,

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

For performance reasons, the Genome Browser automatically condenses the track data into a shorter view mode when viewing many items. From the images you shared, it appears you are looking at a region greater than 2,000 bp, which may be causing the issue. If you want to be able to view these items in 'pack' or 'full', you will have to zoom into a smaller region. However, even after zooming in, there could be more items in the region than allowed by our maxItems trackDb setting.

https://genome.ucsc.edu/goldenpath/help/trackDb/trackDbHub.html#maxItems

We have added a feature request ticket to allow manually setting the maximum items to display before a track automatically condenses. Unfortunately, we do not have an estimated time of completion for this feature, but you can receive email updates about the UCSC Genome Browser by subscribing to our Announcements List:

• Subscribe: Email genome-announce+subs...@soe.ucsc.edu
• Unsubscribe: Email genome-announce+unsub...@soe.ucsc.edu

[Christopher Lee]

Hello Enrique and JP,

Thank you both for your questions about BAM displays. We have created a feature request to allow a "BAM Sampling" view mode, and we will be sure to inform you when/if that mode becomes available.

For now, there are a few potential options. For one, you may be interested in the BAM density mode, which shows the depth of sampling in the form of a wiggle graph. To display your custom track in BAM density mode, navigate to the configuration page for your track by right-clicking on your track and selecting "Configure track", clicking the grey bar on the left side of track image, or click on the track name in the track groups section, and select the checkbox for "Display data as a density graph", which will bring up the usual wiggle configuration options. You will now have a view similar to the following example:
http://genome.ucsc.edu/cgi-bin/hgTracks?hgS_doOtherUser=submit&hgS_otherUserName=chmalee&hgS_otherUserSessionName=hg19_bamDensityExample

You may also be interested in sampling your BAM file via bedtools or another similar tool and then displaying the resulting BAM. Bedtools has a sample command that outputs a BAM:

$ bedtools sample -h

Tool:    bedtools sample (aka sampleFile)
Version: v2.26.0
Summary: Take sample of input file(s) using reservoir sampling algorithm.

Usage:   bedtools sample [OPTIONS] -i <bed/gff/vcf/bam>

Please let us know if you have any further questions,

Christopher Lee
UCSC Genomics Institute

Want to share the Browser with colleagues?
Host a workshop: http://bit.ly/ucscTraining

Thank you again for your inquiry and using the UCSC Genome Browser. 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 forum. If your question includes sensitive data,

you may send it instead to genom...@soe.ucsc.edu.

Want to share the Browser with colleagues?

Host a workshop: http://bit.ly/ucscTraining

• Subscribe: Email genome-announce+subscribe...@soe.ucsc.edu
• Unsubscribe: Email genome-announce+unsubscri...@soe.ucsc.edu

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CADv9Q1B7G8jYW3K4gS5-bPjJxa-Osv9jiezfV6NMWmqJMevpFQ%40mail.gmail.com.