troubleshooting

[Dott.ssa FM Elli]

Hi,

 

the attached custom track in .txt doesn’t work. The genome browser communicates the error message - Expecting at least 5 words line 7 of custom track got 3 – but I don’t understand how to modify it accordingly. Please, may you help me?

Thanks in advance

Francesca

 

Francesca Marta Elli, MS, PhD

Specialista in Genetica Medica

Unità di Endocrinologia e Malattie Metaboliche

Università degli Studi di Milano, Dipt.to di Scienze Cliniche e di Comunità

Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico

Via Pace, 9 – 20122 –Milano

Tel. +39 02 550333512

Fax. +39 02 55033361

cell. +39 3386566220

E-mail: frances...@unimi.it

 

[Jairo Navarro Gonzalez]

Hello Francesca,

Thank you for using the UCSC Genome Browser and your question about using custom tracks. 
The file you provided had an issue on line 7, since you had line break between the chromEnd and the name field for that line. Since BED fields in custom tracks can be whitespace-delimited or tab-delimited, the Browser interprets this line to having only 3 fields (words) rather than 5 compared to the other lines and complains. 
Also, I see that you added dates to the names as well? If so, the browser will interpret the year as the 'score' for that block.
Please change the names to be something like "Fisch_2016" if that is the case.
For your convenience, I have attached a file that loads in the browser and has the changed names.

To learn more about BED file formats, please refer to the BED file format documentation: 
https://genome.ucsc.edu/FAQ/FAQformat.html#format1

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.

Jairo Navarro 
UCSC Genome Browser

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[frances...@unimi.it]

thank you a lot!!!

-------- Messaggio originale --------
Oggetto: Re: [genome] troubleshooting
Da: Jairo Navarro Gonzalez
A: "Dott.ssa FM Elli"
CC: gen...@soe.ucsc.edu

Hello Francesca,

Thank you for using the UCSC Genome Browser and your question about using custom tracks. 
The file you provided had an issue on line 7, since you had line break between the chromEnd and the name field for that line. Since BED fields in custom tracks can be whitespace-delimited or tab-delimited, the Browser interprets this line to having only 3 fields (words) rather than 5 compared to the other lines and complains. 
Also, I see that you added dates to the names as well? If so, the browser will interpret the year as the 'score' for that block.
Please change the names to be something like "Fisch_2016" if that is the case.
For your convenience, I have attached a file that loads in the browser and has the changed names.

To learn more about BED file formats, please refer to the BED file format documentation: 
https://genome.ucsc.edu/FAQ/FAQformat.html#format1

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.

Jairo Navarro 
UCSC Genome Browser

On Wed, Sep 21, 2016 at 1:01 AM, Dott.ssa FM Elli <frances...@unimi.it> wrote:

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