issues with creating custom track

[Courtney Kathleen Ellison]

Hi, 

I am currently revising a paper for the journal Nucleic Acids Research (NAR), and they have a requirement that RNAseq datasets must be viewable via browser format with UCSC indicated as a preferred browser host. I have figured out how to view/map to specific genomes (I am working with the bacterium Acinetobacter baylyi ADP1). I have uploaded my data (bam and bam.bai files) to Zenodo which was recommended by NAR, but I am unable to view my data despite playing around with all of the display settings. I see a gray blank bar with no numerical values/topology. I have attached screenshots of what I see when I do the following: 

Screenshot1 = My data -> Custom tracks

Screenshot2 = My data -> Custom tracks -> Go to first annotation

Screenshot3 = My data -> Custom tracks -> Go to first annotation -> settings icon to the left of the displayed track on the viewer

Here is a link to my Zenodo files: https://zenodo.org/records/17782067?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6Ijc1M2Y4MWZmLTVlNjAtNDFmMy1hMjA2LTMyMjJkM2YxYTc1MyIsImRhdGEiOnt9LCJyYW5kb20iOiJjY2VjMjVhNzU0ZjY4ZWZmYmMzN2JhY2UwN2U2YTQ1MSJ9.jlmy5i4gosCEBloH1ClsA-yXPBlQcm_4hi_VeZBIBe27Ru4KIsAuOnytX-HaFtpyKBgn4gmNwagppw1Am-iNhA

Here is a link to download the first replicate bam file: https://zenodo.org/records/17782067/files/CE100withMMC_rep1.bam?download=1

Here is a link to download the first replicate bam.bai file: https://zenodo.org/records/17782067/files/CE100withMMC_rep1.bam.bai?download=1

I have tried the following which is associated with the gray bar in the screen caps:

track type=bam name="CE100rep1" description="CE100rep1" bigDataUrl=https://zenodo.org/records/17782067/files/CE100withMMC_rep1.bam?download=1 bigDataIndex=https://zenodo.org/records/17782067/files/CE100withMMC_rep1.bam.bai?download=1 doWiggle=<on>

And the following which resulted in the caption 'too many items to display', though zooming in did nothing:

track type=bam name="MMCdata" description="MMCdata" bigDataUrl=https://zenodo.org/records/17782067?token=eyJhbGciOiJIUzUxMiJ9.eyJpZCI6Ijc1M2Y4MWZmLTVlNjAtNDFmMy1hMjA2LTMyMjJkM2YxYTc1MyIsImRhdGEiOnt9LCJyYW5kb20iOiJjY2VjMjVhNzU0ZjY4ZWZmYmMzN2JhY2UwN2U2YTQ1MSJ9.jlmy5i4gosCEBloH1ClsA-yXPBlQcm_4hi_VeZBIBe27Ru4KIsAuOnytX-HaFtpyKBgn4gmNwagppw1Am-iNhA doWiggle=<on>

If you have any guidance or can offer any assistance, I would very greatly appreciate it! 

Courtney

Courtney Ellison, PhD

Assistant Professor

Department of Microbiology

C418 Davison Life Sciences Complex

University of Georgia

[Matthew Speir]

Hello, Courtney.

Thank you for your question about visualizing custom data in the UCSC Genome Browser.

We now provide users with at least 10 GB of hosting space: https://genome.ucsc.edu/cgi-bin/hgHubConnect?#hubUpload. This should fit all the .bam and .bai files you currently have in Zenodo. You could also use the command-line tool bamCoverage to convert your BAM files to bigWigs, which would save quite a bit of space. Alternatively, you could keep the BAM tracks but use the "doWiggle on" setting to have the BAM tracks display in coverage mode by default in the Genome Browser.

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.

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Matthew Speir

UCSC Genome Browser, User Support

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