custom track

[BERY Amandine (VIE)]

Dear UCSC community manager,

I have used to work with table browser and custom track in order to automatically select introns and non coding regions from a list of ENSEMBL gene.

It seems that the option custom track is no more availble in table brower.

Is there any alternative in order to get non coding regions?

Your sincerely

Amandine

[Gerardo Perez]

Hello, Amandine.

Thank you for your interest in the Genome Browser and your question about the custom track option on the Table Browser.

We were unable to replicate your issue. To better assist you, could you provide us with more details, such as the steps and explaining your process? Are using an unofficial mirror? Please ensure you are using one of the mirror sites that we maintain:

http://genome.ucsc.edu
http://genome-euro.ucsc.edu
http://genome-asia.ucsc.edu

I hope this is helpful. Please include gen...@soe.ucsc.edu in any replies to ensure visibility by the team. All messages sent to that address are archived on our public forum. If your question includes sensitive information, you may send it instead to genom...@soe.ucsc.edu.

Gerardo Perez
UCSC Genomics Institute

#6

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[BERY Amandine (VIE)]

Dear Gerardo,

Actually I solved the problem.

First I upload the gene of my interest in My Data. It becomes Custom Track.

Then I go to Table browser and in here GROUP indicates: Custom track.

But comes with a second problem

Using I use Option "Intersect", in order to recover the introns corresponding to the Custom Track. But I doesn't work anymore. Usually I select GROUP: GEne and Gene prediction, then UCSC genes.

Then I select: Base-pair-wise intersection (AND) of Cunstom Track and UCSC Genes 

Finally I select both boxes of "Complement..."

After selection the format (BED) and see resultsin "Galaxy". I select Whole genome.

Unfortunately I get several BED equences that do not correspond to introns.

Can you help

Best regards

Amandine

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De: "Gerardo Perez" <gpe...@ucsc.edu>
À: "BERY Amandine, VIE" <be...@unistra.fr>
Cc: "track-hubs" <track...@soe.ucsc.edu>, "genome" <gen...@soe.ucsc.edu>
Envoyé: Samedi 12 Février 2022 02:00:11
Objet: Re: [genome] custom track

[Gerardo Perez]

Hello, Amandine.

Thank you for your follow-up question.

You can use the Table Browser with some alternative steps to your approach to get the non-coding regions. For example, using Ensembl Genes Identifiers on the Table Browser for hg19:

1. Navigate to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables) and make the following selections:

clade: Mammal
genome: Human
assembly: Dec. 2013 (GRCh37/hg19)
group: Genes and Gene Predictions
track: Ensembl Genes
table: ensGene

2. Set the region to “genome”

3. Click paste list next to “identifiers (names/accessions):” and paste your identifiers. For example:

ENST00000410580
ENST00000369483
ENST00000464464
ENST00000393667
ENST00000435253

then click submit

4. On the Table Browser page, click create next to “intersection:”

5. On the “Intersect with Ensembl Genes” page, make the following selections:

group: Genes and Gene Predictions
track: UCSC Genes
table: UCSC Genes (knownGene)
All Ensembl Genes records that have any overlap with UCSC Genes

then click submit

7. On the Table Browser page, set the output format to “BED - browser extensible data”

8. Select Galaxy

9. Click get output

10. Then on the “Output ensGene as BED” page, select ‘Introns plus’

11. Click Send query to Galaxy

The output will then be available on Galaxy of non-coding regions.

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.

Gerardo Perez
UCSC Genomics Institute