It Appears That You Are Directly Uploading Binary Data in an Unrecognized Format .bam

Jai Nagpal

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24 Mar 2021 04.37.22 24/03/21

kepadagen...@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 information in an unrecognized format. For custom track formatting data, delight see custom track documentation."

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

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

Whatever feedback would be greatly appreciated.

Sincerely,

Jai Nagpal

Brian Lee

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24 Mar 2021 04.39.35 24/03/21

kepadaJai Nagpal, UCSC Genome Browser Mailing Listing, Vandenbergh, David John

Honey Jai Nagpal,

Thanks for using the UCSC Genome Browser and your question virtually this new mistake regarding custom track uploading.

We have seen something similar in recent users where silent encoding is causing difficulties in uploading runway data, more oftentimes with hidden encoding on whitespaces. We have a issues ticket to investigate this development farther, and your case has been added to the ticket and may help united states detect the issue ameliorate.

Taking a look at your shared data, by ensuring the information is in plain text format it appears the quotes effectually the description are encoded. Description elements if they are without spaces (non description="This is my long description") tin can be declared with only the equal sign (description=Primers), so try that in your custom track:

rail name=Primers type=bedDetail description=Primers visibility=2 colour=221,55,1

By making that alter I had success uploading the manifestly text version of your file and even so having the browser line included. I did note that the concluding row in the information 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 bulletin would display to catch that issue).

Thank you again for your inquiry and using the UCSC Genome Browser. If y'all accept any farther public questions, please respond to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

All the all-time,

--

Vandenbergh, David John

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24 Mar 2021 09.55.41 24/03/21

kepadaBrian Lee, nagpa...@gmail.com, UCSC Genome Browser Mailing Listing

Wow, thanks for the rapid response, Brian. Is there a formatting option inside Apple's TextEdit that leaves out the problematic codes, or mayhap some other app that is ameliorate 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

Hiram Clawson

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24 Mar 2021 x.18.10 24/03/21

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

Good Evening David:

When in textedit, use the 'Format' pull downwards carte
and select the option 'Brand Plain Text'

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

Likewise accessed via the keystroke: Shift-Command-T

--Hiram

On three/23/21 7:51 PM, Vandenbergh, David John wrote:
> Wow, thanks for the rapid response, Brian. Is there a formatting option 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 Constitute
> 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 nearly this new error regarding custom rails uploading.
>
> We have seen something like in recent users where silent encoding is causing difficulties in uploading rail data, more often with hidden encoding on whitespaces. We accept a problems ticket to investigate this evolution further, and your example has been added to the ticket and may assistance united states discover the issue ameliorate.
>
> Taking a wait at your shared information, past ensuring the data is in plain text format it appears the quotes around the clarification are encoded. Clarification elements if they are without spaces (not description="This is my long description") tin can be declared with just the equal sign (description=Primers), and so effort that in your custom track:
>
> track proper name=Primers type=bedDetail description=Primers visibility=2 color=221,55,one
>
> Past making that change I had success uploading the obviously text version of your file and still having the browser line included. I did note that the final row in the data had an outcome 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 fault bulletin would display to catch that issue).
>

> Thank you again for your inquiry and using the UCSC Genome Browser. If you take any farther 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, yous may send information technology 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:
> Dearest 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 fastened in this email.
>
> I recently updated the text file and tried to upload to the genome browser by copying/pasting, when I received an fault bulletin saying the following: "It appears that yous are direct uploading binary data in an unrecognized format. For custom rails formatting information, please see custom rail 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 whatever mistake bulletin.
> I'm unsure why this line would cause an error, specially since I've uploaded this file several times in the past without whatever effect.
>
> Any feedback would be greatly appreciated.
>
> Sincerely,
> Jai Nagpal
>
> --
>
> ---
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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>
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Brian Lee

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24 Mar 2021 10.24.00 24/03/21

kepadaVandenbergh, David John, nagpa...@gmail.com, UCSC Genome Browser Mailing Listing

Dear David,

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

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

Then, there is one additional subconscious encoding yet happening at the beginning of the file. If you click into the plain text file and delete the word rail (in patently text way) and retype rail (mainly just the start alphabetic character needed deleting to remove a ^Htrack encoding) you volition remove the encoding at the showtime of the file. So the file should piece of work to upload.

All the best,
Brian

Vandenbergh, David John

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24 Mar 2021 22.57.54 24/03/21

kepadaHiram Clawson, Brian Lee, nagpa...@gmail.com, UCSC Genome Browser Mailing Listing

Thanks Hiram,

We'll endeavor it out and volition 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

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

Good Evening David:

When in textedit, apply the 'Format' pull down card
and select the choice 'Make Plain Text'

Vandenbergh, David John

belum dibaca,

24 Mar 2021 22.58.36 24/03/21

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

Thanks Brian!

David

Jai, why don't you endeavour it and and so 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

Jai Nagpal

belum dibaca,

25 Mar 2021 06.31.32 25/03/21

kepadaBrian Lee, Vandenbergh, David John, UCSC Genome Browser Mailing Listing, 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 nonetheless receiving the same error message every bit before.

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

Our lab does take a written protocol to aid members create/edit custom tracks. Information technology will demand to be updated to incorporate the changes you lot have suggested, merely our electric current version is fastened.

Thank you all for your help, and please allow me know if you demand more than information.

Jai

PCR_Experimental_Custom_Track_Instructions.docx

Brian Lee

belum dibaca,

25 Mar 2021 12.25.50 25/03/21

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

Beloved Jai and David,

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

Jumping to the step 34, where y'all would paste in the information in the file and everything would work. I added a few steps where y'all proceed to paste in the information, but you hit submit first in one case, 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 summit comment line (generated to help reduce the display) and the first word "track" that has the hidden encoding).

34. Copy and paste the lawmaking section created to a higher place into the text box entitled "Paste URLs or information:".
35. Re-create and paste the description section created above into the text box entitled "Optional track documentation:".
36. Click the "submit" button near the upper right-paw corner of the first text box.
37. Ignore the " Mistake Information technology 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 pace.
38. Click into the "Paste URLs or data:" box and delete the first line displaying "# Displaying first fifty lines of data" and the showtime word of the second line, "rails".
39. Blazon "track" back into the window where you removed it, this will insert a fresh version of the word "rails" and remove hidden encoding that was triggering the previous error message.
40. Click the "submit" button almost 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 footstep 38 about deleting the text to make information technology clear what expanse to remove.

All the best,

Vandenbergh, David John

belum dibaca,

25 Mar 2021 23.21.49 25/03/21

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

Hi Brian,

Practice I assume correctly that nosotros tin also type in the line for browser position when we retype the discussion rail? Information technology is very nice to take that line to direct the browser to a window of a certain size, rather than defaulting to the first item, which is normally 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

Jai Nagpal

belum dibaca,

27 Mar 2021 00.56.51 27/03/21

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

Dr. 5,

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

Thank you lot Brian! I actually appreciate all you've done to help and explain how to solve this effect for us!

Jai

Daniel Schmelter

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27 Mar 2021 06.10.03 27/03/21

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

How-do-you-do Jai and David,

I'm glad Brian's proposition worked for you lot. In response to your question about the browser lines, you should be able to blazon those in as expected. The mistake here seems to be a re-create-paste issue, so typing any position in should be simply fine. For reference, the browser lines are documented below:

browser position chr22:1-2000

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

Warmly,

Daniel Schmelter

UCSC Genome Browser

davistwouldes1954.blogspot.com

Source: https://groups.google.com/a/soe.ucsc.edu/g/genome/c/raeIf5TA_v4