Uploading Custom Track Error Message

Jai Nagpal

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Mar 23, 2021, 5:37:22 PM3/23/21

to gen...@soe.ucsc.edu, Vandenbergh, David John

Dear Team,

My name is Jai and I have regularly updated a custom track containing the positions of primers that my lab uses for PCR experiments.

The custom track is saved in a text file in bedDetail format that I've attached in this email.

I recently updated the text file and tried to upload to the genome browser by copying/pasting, when I received an error message saying the following: "It appears that you are directly uploading binary data in an unrecognized format. For custom track formatting information, please see custom track documentation."

Interestingly, when I remove just the top line of the text file, "browser position chr5 1405000-1448000", I am able to upload the custom track without any error message.

I'm unsure why this line would cause an error, especially since I've uploaded this file several times in the past without any issue.

Any feedback would be greatly appreciated.

Sincerely,

Jai Nagpal

Lab Primers.rtf

Brian Lee

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Mar 23, 2021, 5:39:35 PM3/23/21

to Jai Nagpal, UCSC Genome Browser Mailing List, Vandenbergh, David John

Dear Jai Nagpal,

Thank you for using the UCSC Genome Browser and your question about this new error regarding custom track uploading.

We have seen something similar in recent users where silent encoding is causing difficulties in uploading track data, more often with hidden encoding on whitespaces. We have a bug ticket to investigate this development further, and your case has been added to the ticket and may help us detect the issue better.

Taking a look at your shared data, by ensuring the data is in plain text format it appears the quotes around the description are encoded. Description elements if they are without spaces (not description="This is my long description") can be declared with just the equal sign (description=Primers), so try that in your custom track:

track name=Primers type=bedDetail description=Primers visibility=2 color=221,55,1

By making that change I had success uploading the plain text version of your file and still having the browser line included. I did note that the final row in the data had an issue and had to remove that line, "chr11 642933 642915 hDRD4642934R...". In that single row 642,933 is greater than 642,915 where chromStart needs to be less than chromEnd (an error message would display to catch that issue).

Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public 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.

All the best,

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Vandenbergh, David John

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Mar 23, 2021, 10:55:41 PM3/23/21

to Brian Lee, nagpa...@gmail.com, UCSC Genome Browser Mailing List

Wow, thanks for the rapid response, Brian. Is there a formatting choice within Apple's TextEdit that leaves out the problematic codes, or perhaps another app that is better suited for the purpose?

David

David J. Vandenbergh, Ph.D.

Professor, Dept. of Biobehavioral Health
Penn State Neuroscience Institute

Mol., Cell., & Integrative Biosciences

Bioinformatics & Genomics

258A Health & Hum Dev Bld (HHD)
Tel 814-863-8430
Lab 814-863-1325
http://sites.psu.edu/vandenberghlab/

From: Brian Lee <bria...@soe.ucsc.edu>
Sent: Tuesday, March 23, 2021 5:38 PM
To: nagpa...@gmail.com <nagpa...@gmail.com>
Cc: UCSC Genome Browser Mailing List <gen...@soe.ucsc.edu>; Vandenbergh, David John <dj...@psu.edu>
Subject: Re: [genome] Uploading Custom Track Error Message

Hiram Clawson

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Mar 23, 2021, 11:18:10 PM3/23/21

to Vandenbergh, David John, Brian Lee, nagpa...@gmail.com, UCSC Genome Browser Mailing List

Good Evening David:

When in textedit, use the 'Format' pull down menu
and select the option 'Make Plain Text'

https://www.iphonehacks.com/2017/06/plain-text-mode-textedit-mac.html

Also accessed via the keystroke: Shift-Command-T

--Hiram

On 3/23/21 7:51 PM, Vandenbergh, David John wrote:
> Wow, thanks for the rapid response, Brian. Is there a formatting choice within Apple's TextEdit that leaves out the problematic codes, or perhaps another app that is better suited for the purpose?
> David
>
>
>
> David J. Vandenbergh, Ph.D.
>
> Professor, Dept. of Biobehavioral Health
> Penn State Neuroscience Institute
> Mol., Cell., & Integrative Biosciences
> Bioinformatics & Genomics
> 258A Health & Hum Dev Bld (HHD)
> Tel 814-863-8430
> Lab 814-863-1325
> http://sites.psu.edu/vandenberghlab/
>
>
> ________________________________
> From: Brian Lee <bria...@soe.ucsc.edu>
> Sent: Tuesday, March 23, 2021 5:38 PM
> To: nagpa...@gmail.com <nagpa...@gmail.com>
> Cc: UCSC Genome Browser Mailing List <gen...@soe.ucsc.edu>; Vandenbergh, David John <dj...@psu.edu>
> Subject: Re: [genome] Uploading Custom Track Error Message
>
> Dear Jai Nagpal,
>
> Thank you for using the UCSC Genome Browser and your question about this new error regarding custom track uploading.
>
> We have seen something similar in recent users where silent encoding is causing difficulties in uploading track data, more often with hidden encoding on whitespaces. We have a bug ticket to investigate this development further, and your case has been added to the ticket and may help us detect the issue better.
>
> Taking a look at your shared data, by ensuring the data is in plain text format it appears the quotes around the description are encoded. Description elements if they are without spaces (not description="This is my long description") can be declared with just the equal sign (description=Primers), so try that in your custom track:
>
> track name=Primers type=bedDetail description=Primers visibility=2 color=221,55,1
>
> By making that change I had success uploading the plain text version of your file and still having the browser line included. I did note that the final row in the data had an issue and had to remove that line, "chr11 642933 642915 hDRD4642934R...". In that single row 642,933 is greater than 642,915 where chromStart needs to be less than chromEnd (an error message would display to catch that issue).
>

> Thank you again for your inquiry and using the UCSC Genome Browser. If you have any further public questions, please reply to gen...@soe.ucsc.edu<mailto: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<mailto:genom...@soe.ucsc.edu>.
>
> All the best,

>
> On Tue, Mar 23, 2021 at 2:37 PM Jai Nagpal <nagpa...@gmail.com<mailto:nagpa...@gmail.com>> wrote:
> Dear Team,
>
> My name is Jai and I have regularly updated a custom track containing the positions of primers that my lab uses for PCR experiments.
> The custom track is saved in a text file in bedDetail format that I've attached in this email.
>
> I recently updated the text file and tried to upload to the genome browser by copying/pasting, when I received an error message saying the following: "It appears that you are directly uploading binary data in an unrecognized format. For custom track formatting information, please see custom track documentation."
>
> Interestingly, when I remove just the top line of the text file, "browser position chr5 1405000-1448000", I am able to upload the custom track without any error message.
> I'm unsure why this line would cause an error, especially since I've uploaded this file several times in the past without any issue.
>
> Any feedback would be greatly appreciated.
>
> Sincerely,
> Jai Nagpal
>
> --
>
> ---
> You received this message because you are subscribed to the Google Groups "UCSC Genome Browser Public Support" group.

> To unsubscribe from this group and stop receiving emails from it, send an email to genome+un...@soe.ucsc.edu<mailto:genome+un...@soe.ucsc.edu>.
> To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CALEN9QCPiLXJukhhVSAE-jk1rm3L755KivqwXpHcSGbrsFvWKw%40mail.gmail.com<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgroups.google.com%2Fa%2Fsoe.ucsc.edu%2Fd%2Fmsgid%2Fgenome%2FCALEN9QCPiLXJukhhVSAE-jk1rm3L755KivqwXpHcSGbrsFvWKw%2540mail.gmail.com%3Futm_medium%3Demail%26utm_source%3Dfooter&data=04%7C01%7Cdjv4%40psu.edu%7C7b9ca67e7ea845fff6d508d8ee44261d%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637521323759291895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=zDPVjBzRxPot0eR8xarT41lYE%2FfuV6LRMz7Hqwq22ms%3D&reserved=0>.
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>
> --
> Brian Lee
> UCSC Genome Browser<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenome.ucsc.edu%2F&data=04%7C01%7Cdjv4%40psu.edu%7C7b9ca67e7ea845fff6d508d8ee44261d%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637521323759301895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=7az2opxT74SB8olWtwPaMy%2BvEJiGoXYbibfILh7la4o%3D&reserved=0>
> UC Santa Cruz Genomics Institute<https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgenomics.ucsc.edu%2F&data=04%7C01%7Cdjv4%40psu.edu%7C7b9ca67e7ea845fff6d508d8ee44261d%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637521323759301895%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=M6E6eeRgaImVr0rC6M9LFcVOUnWUevYRO3BRxDW1bCU%3D&reserved=0> | Revealing life’s code.
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Brian Lee

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Mar 23, 2021, 11:24:00 PM3/23/21

to Vandenbergh, David John, nagpa...@gmail.com, UCSC Genome Browser Mailing List

Dear David,

I apologize for this frustrating experience around the encoding. It does look like there is a way with TextEdit in Mac to remove the encoding, but it takes one additional step.

When you have the original file you shared, open it in TextEdit and then go to the Format option and then select the "Make Plain Text" (or Shfit+Command+T) to toggle back and forth between plain text and rich text.

Then, there is one additional hidden encoding still happening at the beginning of the file. If you click into the plain text file and delete the word track (in plain text mode) and retype track (mainly just the first letter needed deleting to remove a ^Htrack encoding) you will remove the encoding at the start of the file. Then the file should work to upload.

All the best,
Brian

Vandenbergh, David John

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Mar 24, 2021, 11:57:54 AM3/24/21

to Hiram Clawson, Brian Lee, nagpa...@gmail.com, UCSC Genome Browser Mailing List

Thanks Hiram,

We'll try it out and will add those steps to our lab's protocol.

David

David J. Vandenbergh, Ph.D.

Professor, Dept. of Biobehavioral Health
Penn State Neuroscience Institute

Mol., Cell., & Integrative Biosciences

Bioinformatics & Genomics

258A Health & Hum Dev Bld (HHD)
Tel 814-863-8430
Lab 814-863-1325
http://sites.psu.edu/vandenberghlab/

From: Hiram Clawson <hi...@soe.ucsc.edu>
Sent: Tuesday, March 23, 2021 11:18 PM
To: Vandenbergh, David John <dj...@psu.edu>; Brian Lee <bria...@soe.ucsc.edu>; nagpa...@gmail.com <nagpa...@gmail.com>

Cc: UCSC Genome Browser Mailing List <gen...@soe.ucsc.edu>

Subject: Re: [genome] Uploading Custom Track Error Message

Good Evening David:

When in textedit, use the 'Format' pull down menu
and select the option 'Make Plain Text'

https://nam10.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.iphonehacks.com%2F2017%2F06%2Fplain-text-mode-textedit-mac.html&data=04%7C01%7Cdjv4%40psu.edu%7C0b974e3bcdbe4cc2280108d8ee737149%7C7cf48d453ddb4389a9c1c115526eb52e%7C0%7C1%7C637521526883979695%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C2000&sdata=e0ecpaCslEG%2BNAKCDR5f9F2gkdAgVJtvs2itCf1fzjI%3D&reserved=0

Vandenbergh, David John

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Mar 24, 2021, 11:58:36 AM3/24/21

to Brian Lee, nagpa...@gmail.com, UCSC Genome Browser Mailing List

Thanks Brian!

David

Jai, why don't you try it and then add those steps to our lab's protocol.

David J. Vandenbergh, Ph.D.

Professor, Dept. of Biobehavioral Health
Penn State Neuroscience Institute

Mol., Cell., & Integrative Biosciences

Bioinformatics & Genomics

258A Health & Hum Dev Bld (HHD)
Tel 814-863-8430
Lab 814-863-1325
http://sites.psu.edu/vandenberghlab/

From: Brian Lee <bria...@soe.ucsc.edu>
Sent: Tuesday, March 23, 2021 11:23 PM

To: Vandenbergh, David John <dj...@psu.edu>

Cc: nagpa...@gmail.com <nagpa...@gmail.com>; UCSC Genome Browser Mailing List <gen...@soe.ucsc.edu>

Jai Nagpal

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Mar 24, 2021, 7:31:32 PM3/24/21

to Brian Lee, Vandenbergh, David John, UCSC Genome Browser Mailing List, mhae...@ucsc.edu

Hello All,

I've gone ahead and made changes to our original text file, including switching it to a plain text format and deleting then retyping the word "track" to remove additional encoding, but I am still receiving the same error message as before.

I've attached the updated file, could you see if there is something I've missed?

Our lab does have a written protocol to help members create/edit custom tracks. It will need to be updated to incorporate the changes you have suggested, but our current version is attached.

Thank you all for your help, and please let me know if you need more information.

Jai

PCR_Experimental_Custom_Track_Instructions.docx

Lab Primers.rtf

Brian Lee

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Mar 25, 2021, 1:25:50 AM3/25/21

to Jai Nagpal, Vandenbergh, David John, UCSC Genome Browser Mailing List, Maximilian Haeussler

Dear Jai and David,

Thank you for sharing the steps it helped to replicate the process being taken. Again,I apologize for this frustrating experience around the encoding. Now that I see the cut-and-paste process in your notes I can suggest these steps that should work (they worked for me with the original file shared in the original email (Lab Primers.rtf).

Jumping to the step 34, where you would paste in the data in the file and everything would work. I added a few steps where you continue to paste in the data, but you hit submit first once, this will trigger the "binary data" error message. Then the new step is to click into the window on the Custom Track page and to remove the top comment line (generated to help reduce the display) and the first word "track" that has the hidden encoding).

34. Copy and paste the code section created above into the text box entitled “Paste URLs or data:”.
35. Copy and paste the description section created above into the text box entitled “Optional track documentation:”.
36. Click the “submit” button near the upper right-hand corner of the first text box.
37. Ignore the " Error It appears that you are directly uploading binary data " message. This comes from hidden encoded text in the pasted data that can be removed with the next step.
38. Click into the “Paste URLs or data:” box and delete the first line displaying "# Displaying first 50 lines of data" and the first word of the second line, "track".
39. Type "track" back into the window where you removed it, this will insert a fresh version of the word "track" and remove hidden encoding that was triggering the previous error message.
40. Click the “submit” button near the upper right-hand corner of the first text box.

Please let me know if that works for the protocol. Here is a picture for step 38 about deleting the text to make it clear what area to remove.

All the best,

Vandenbergh, David John

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Mar 25, 2021, 12:21:49 PM3/25/21

to Brian Lee, nagpa...@gmail.com, UCSC Genome Browser Mailing List, Maximilian Haeussler

Hi Brian,

Do I assume correctly that we can also type in the line for browser position when we retype the word track? It is very nice to have that line to direct the browser to a window of a certain size, rather than defaulting to the first item, which is usually only a 20 bp primer.

Thanks,

David

David J. Vandenbergh, Ph.D.

Professor, Dept. of Biobehavioral Health
Penn State Neuroscience Institute

Mol., Cell., & Integrative Biosciences

Bioinformatics & Genomics

258A Health & Hum Dev Bld (HHD)
Tel 814-863-8430
Lab 814-863-1325
http://sites.psu.edu/vandenberghlab/

From: Brian Lee <bria...@soe.ucsc.edu>
Sent: Thursday, March 25, 2021 1:25 AM
To: nagpa...@gmail.com <nagpa...@gmail.com>
Cc: Vandenbergh, David John <dj...@psu.edu>; UCSC Genome Browser Mailing List <gen...@soe.ucsc.edu>; Maximilian Haeussler <mhae...@ucsc.edu>

Jai Nagpal

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Mar 26, 2021, 1:56:51 PM3/26/21

to Vandenbergh, David John, Brian Lee, UCSC Genome Browser Mailing List, Maximilian Haeussler

Dr. V,

Following Brian's instructions, I was able to enter the data into the custom track successfully, including the browser position line. This means that we won't have to zoom out of the browser's position each time we update the custom track.

Thank you Brian! I really appreciate all you've done to help and explain how to solve this issue for us!

Jai

Daniel Schmelter

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Mar 26, 2021, 7:10:03 PM3/26/21

to Jai Nagpal, Vandenbergh, David John, Brian Lee, UCSC Genome Browser Mailing List, Maximilian Haeussler

Hello Jai and David,

I'm glad Brian's suggestion worked for you. In response to your question about the browser lines, you should be able to type those in as expected. The error here seems to be a copy-paste issue, so typing any position in should be just fine. For reference, the browser lines are documented below:

browser position chr22:1-2000

http://genome.ucsc.edu/goldenPath/help/customTrack.html#BROWSER

Let us know if you have any other questions and we will do our best to help. Reply-all to gen...@soe.ucsc.edu to ensure visibility by our whole team. All messages sent to that address are publicly archived. If your question includes sensitive data, please reply-all to genom...@soe.ucsc.edu.

Warmly,

Daniel Schmelter

UCSC Genome Browser

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/CALEN9QA2OdnxG12Quj4U7eQAiC6GWq52MrpykJUubV-UmypwHA%40mail.gmail.com.

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