UCSC browser custom tracks: does not recognize bai file

[Anandakrishnan, Ramu]

Hello,

 

I’m trying to setup a custom track for my sequencing data as required for NAR submission. I have my data on Google Drive and I used the following command to load the data:

 

track type=bam name="exochew-ecoli bam" bigDataUrl=https://drive.google.com/file/d/1kSq31NCZ9SVCsX7OlxVc8ek77NCmlueh/view?usp=sharing bigDataIndex=https://drive.google.com/file/d/1F5qLqZdlYsIRJl8hexPD4V7qKWY2etnG/view?usp=sharing

 

It seems to be ok with the bam file, but I get the following error for the bai file:

 

: failed to read index file (.bai) corresponding to https://drive.google.com/file/d/1kSq31NCZ9SVCsX7OlxVc8ek77NCmlueh/view?usp=sharing

 

Thanks for your help.

Best,

Ramu Anandakrishnan

 

[Luis Nassar]

Hello.

Unfortunately, the way Google Drive provides access to the data is not compatible with our system.

We offer a few options on our hosting page (https://genome.ucsc.edu/goldenPath/help/hgTrackHubHelp#Hosting). Either CyVerse Discovery Environment or Galaxy could be a solution, but we are also trialing a new feature that allows users to upload their custom data for visualization.

You can upload your files to our live trial server here by logging into your UCSC Genome Browser user (https://hgw0.soe.ucsc.edu/cgi-bin/hgHubConnect#hubUpload). Once you do, you should be able to visualize the track.

However, it looks like your reads are aligned to the following E. Coli assembly (GCF_000019425.1), is that correct?

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Lou Nassar
UCSC Genomics Institute