uploading data in UCSC Microbial genome browser

Question

[vimlakany]

Hi

I have *_sorted.bam file (prokaryotic/RNA seq) which i want to upload from my local machine (not making it publicly accessible) to UCSC microbial genome browser and visualize its expression.

I tried uploading it through 'add custom track' by converting bamtobigwig file format, then i am getting an error as below:

" Error File '*.bigwig' - It appears that you are directly uploading binary data in an unrecognized format. For custom track formatting information, please see custom track documentation. "

Can anyone please suggest me how to upload data from my machine (not making it publicly accessible) to custom track in UCSC microbial genome browser for visualizing the expression of RNA seq data

[GenoMax]

Based on this FAQ bigwig may not be supported on UCSC Microbial genome browser.

[vimlakany]

I tried with .BED format file also, still i am getting the same error. So now what should i do to upload?

[GenoMax]

BED data is not binary so if you are getting the same error then something is not correct.

[Satyajeet Khare]

You may need an index file (.bai). You might be able to upload the BAM file directly. Else, you can try an offline browsers such as IGV.

Answer 1

[Matthew_UCSC]

You cannot directly upload binary files, such as bigWig, bigBed, or BAM, directly to the Genome Browser. If you want to use bigWig then you must place the file on a publicly-accessible web server and then provide the URL to that location to the Genome Browser. See the bigWig format page: https://genome.ucsc.edu/goldenPath/help/bigWig.html.

You can convert your data back to "wiggle" format and then upload that to the Genome Browser. You would use the bigWigToWig tool located on the UCSC Genome Browser download server here: http://hgdownload.soe.ucsc.edu/admin/exe/. And then upload it as a custom track according to the examples/instructions on these pages:

• https://genome.ucsc.edu/goldenPath/help/wiggle.html
• https://genome.ucsc.edu/goldenPath/help/customTrack.html

[GenoMax]

Matthew_UCSC : Original post is about UCSC Microbial genome browser not the standard one.

[Matthew_UCSC]

That's true, but they are both based on the same software and so the pages on the UCSC Genome Browser's main site should be relevant to the Microbial Genome Browser. (Though I believe that the Microbial Browser is a few versions behind the main UCSC Genome Browser.)

Here are the same pages on the Microbial website:

• "BigWig" format: http://microbes.ucsc.edu/goldenPath/help/bigWig.html
• "Wiggle" format: http://microbes.ucsc.edu/goldenPath/help/wiggle.html
• "Custom Track User Guide": http://microbes.ucsc.edu/goldenPath/help/customTrackText.html (Unfortunately, it looks like something is wrong with the full HTML page, but this is the contents of it.)

They should be nearly identical.

You can also contact Todd Lowe, who runs the Microbial Browser if you are having any issues with their site: http://lowelab.ucsc.edu/contact.html.

[GenoMax]

Thank you for the clarification. FAQ on Microbial browser site had restricted support for file formats so I wanted to make sure.

[vimlakany]

Thank you for your reply sir,

In UCSC Microbial genome browser, for eg. if I want to view Mycobacterium smegmatis MC2 155 annotation, the page appears blank & I am not able to view the annotations.

http://microbes.ucsc.edu/cgi-bin/hgTracks?db=mycoSmeg_MC2_155&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr%3A10001%2D35000&hgsid=2613038_iPZAKTpGdrVg3XGCEIuCtsBzj2XK

Is this a problem with UCSC microbial genome browser?

but in case of UCSC genome browser I am able to view the annotations.

[Matthew_UCSC]

Yeah, that appears to be an issue with the Microbial Browser. You should contact Todd Lowe to bring this to his attention: http://lowelab.ucsc.edu/contact.html.

The Genome Browser (https://genome.ucsc.edu) and the Microbial Browser (http://microbes.ucsc.edu/) are run by two different groups. The Genome Browser by its own set of staff, https://genome.ucsc.edu/staff.html, and the Microbial Browser by Todd and his group, http://lowelab.ucsc.edu/people.html.