Table browsr Mouse Genome

[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 browser.

However you (Gerardo Perez) gave me an alternative that works for human genome. Unfortunately I work with mouse genome (mm10).

Actually, when I choose "Genes and Gene predictions, then I cannot select "ensembl Genes " as track. This option exists only in human.

What is the option that allow me to upload my list of Ensembl genes from which I want to extract non-coding regions?

Your sincerely

Amandine

[Brian Lee]

Hello, Amandine.

Thank you for your follow-up question. You can use the GENCODE gene set and apply Ensembl identifiers. The two gene sets are basically the same: http://genome.ucsc.edu/FAQ/FAQgenes.html#ens

For example, using Ensembl Genes Identifiers on the Table Browser for mm39:

1. Navigate to the Table Browser (http://genome.ucsc.edu/cgi-bin/hgTables?db=mm39) and make the following selections:

    clade: Mammal
    genome: Mouse
    assembly: Jun. 2020 (GRCm39/mm39)
    group: Genes and Gene Predictions
    track: GENCODE VM27
    table: knownGene

2. Set the region to “genome”

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

   ENSMUST00000189167.7
   ENSMUST00000139468.2
   ENSMUST00000191347.7

    then click submit

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

5. On the “intersection with knownGene” page, make the following selections:

    group: Genes and Gene Predictions
    track: GENCODE VM27
    table: knownGene
    All GENCODE VM27 records that have any overlap with GENCODE VM27 

    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 knownGene as BED” page, select "Introns plus"

11. Click Send query to Galaxy

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

You can also set the output to a custom track (at step 10: set to "custom track" and then don't click the Galaxy button in 11, and rather click "get output" and "get custom track in genome browser") to look at the results, here is an example session of those results from the above steps: http://genome.ucsc.edu/s/brianlee/Introns

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.

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[BERY Amandine (VIE)]

Dear Brian Lee,

I have follow your instructions (see message below).

However some sequences are incorrectly selected.

For example, by using the gene Dlg2 (mm39) the resulting uncoding regions include also coding region (cf the 1st region of the attached file include coding region of Dlg2).

Moreover, the list appears to be incomplet (cf the last region of the attached file isn't the last uncoding region of Dlg2).

How is it possible to solve the problem?

Should I do it manually?

Many thanks

Amandine

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De: "Brian Lee" <bria...@soe.ucsc.edu>
À: "BERY Amandine, VIE" <be...@unistra.fr>
Cc: "UCSC Genome Browser Mailing List" <gen...@soe.ucsc.edu>
Envoyé: Mercredi 23 Février 2022 20:12:43
Objet: Re: [genome] Table browsr Mouse Genome

[Gerardo Perez]

Hello, Amandine.

Thank you for your follow-up question and for providing the attached file.

We uploaded the data from your file as a custom track and compared the annotation data to the Dlg2 gene. It looks like the reason you are viewing the 1st exon as non-coding is due to the subtracks in the Gencode M27 track. By default, the Gencode M27 track shows the Basic subtrack. If you enable the Comprehensive subtrack, you will see the other transcripts, one of which (ENSMUST00000208919.2) has an upstream exon causing that transcript's first intron to span the first intron of the Basic track's only transcript (ENSMUST00000231777.3). Here is a session that shows this:
http://genome.ucsc.edu/s/gperez2/mlq_28952

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

To view this discussion on the web visit https://groups.google.com/a/soe.ucsc.edu/d/msgid/genome/8352838.12294570.1680173350329.JavaMail.zimbra%40unistra.fr.