Britta M
"The basic overview of what we will do here is take your track data and use the Table Browser to create a custom track that just contains the introns from your data. Then we will use the Table Browser a second time to generate GTF output from that custom track.
1. Load your data file as a custom track.
2. Open the UCSC Table Browser at http://genome.ucsc.edu/cgi-bin/hgTracks and select your custom track.
3. Set up any region and identifier filters that you want to impose (or just set the region to "genome"), and set the output format to "custom track".
4. Click "get output".
5. On the next page, name your new custom track (e.g., "introns from my data") and select the box to create one BED record per "Introns plus 0 bases on each end".
6. Click "get custom track in table browser". You should now be returned to the main UCSC Table Browser page.
7. Select your new custom track from the menu (e.g., Group: Custom Tracks, Track: introns from my data).
8. Change the output format to "GTF - gene transfer format".
9. Click "get output".
The result should be a GTF file that describes the intron regions of your data."
Cath Tyner
Hi Britta,
Thank you for contacting the UCSC Genome Browser support team. I'm not quite sure what you are asking. In order to best support you, could you provide more information? Can you respond to this forum with the following information:
1. Please list exactly which fields you would like to see in your output. If you can provide an example of the output file you would like, that would be best.
2. Please describe which assembly and which track you would like to get output for.
I'm not sure if this answers your question, but here is a previously answered question which described how to select fields from related tables for Table Browser output, such as gene alias and exon count.
Also, here is documentation about the genePred file format. Most of the gene track tables are in genePred format. If you follow the steps in the previously answered question above, you will see an example of how to select and remove certain fields from your Table Browser output, including fields such as gene alias.
If your response contains confidential information, you can reply directly to me. Otherwise, please respond to this forum with more information so that our support team can provide specific help for you.
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Cath Tyner
Thank you for writing back and including clarification on your question. I will provide some steps below which I hope will help you meet your goal. If I have misunderstood your goal, or if you have further questions, please feel free to write back again!
Converting genePred to GTF
You can convert genePred to GTF by following the instructions here: http://genomewiki.ucsc.edu/index.php/Genes_in_gtf_or_gff_format
Once you have downloaded the genePredToGtf utility (and given execute permissions), you can run the command:
$ genePredToGtf
Which will output the usage statement.
You can then use the command:
$ genePredToGtf gasAcu1 ensGene ensGene.gtf
Which will provide output like this by connecting to the UCSC Genome Browser database/tables:Note that the gene name is included in the gtf output because this ensGene table includes the extended file format (fields beyond the genPred format).
This gtf file of the ensGene table for gasAcu1 is available for you to download here:
http://hgwdev.cse.ucsc.edu/~cath/temp/gasAcu1ensGene.gtf
Or, if you only want chrUn for gasAcu1, use this file:
http://hgwdev.cse.ucsc.edu/~cath/temp/ensGeneChrUnOnly.gtf
If the above gtf file is not what you want, you can customize fields in the Table Browser. Below are examples to get all fields for the ensGene table, as well as an example to add/remove fields.
1. Go to the Table Browser at the UCSC Genome Browser and configure as follows:
http://genome.ucsc.edu/cgi-bin/hgTables
clade: Vertebrategenome: Sticklebackassembly: gasAcu1group: Genes & Gene Predictionstrack: Ensembl Genestable: ensGeneregion: you can select "genome" or a particular region, such as "chrUn:1-62550211" for the entire chrUn.
The ensGene table stores values in the genePred extended data format. https://genome.ucsc.edu/FAQ/FAQformat.html#format9
In the Table Browser, you can click on "describe table schema" to see the table description:
http://genome.ucsc.edu/cgi-bin/hgTables?hgta_doSchemaDb=gasAcu1&hgta_doSchemaTable=ensGene
2. After viewing the table schema, if there are other fields you would like to add, or if there are fields you would like to remove from the output, change the "output format" drop-down to "selected fields from primary and related tables."
Otherwise, if you want all fields in the table and have no other fields to add, keep the "output format" drop-down as "all fields from selected table."
If you selected "all fields from selected table" from "output format" you will get output like this:Note: to get this output in the browser, leave the "output file" field blank. To get output as a downloaded file, enter a name for the file in that field.
If, however, you would like to add or remove fields from either the ensGene table or from a related table, you can follow the example below:
Change the "output format" drop-down to "selected fields from primary and related tables."
Click "get output" to go to the next step.
Select the fields that you would like from the ensGene table. In this example, I'll select all fields except for "bin."
If you don't want to include fields from other tables, you can now click, "get output."
Otherwise, under the section, "Linked Tables" select 1 or more linked tables and then click, "allow selection from checked tables".
You can select all of the related tables for now, and then simply choose whichever fields you want to add. For this example, I'll add the following table.fields and then click "get output".
- ensemblSource.source
- ensemblToGeneName.value
You will now get output like this, where we've removed "ensGene.bin" and added "ensGtp.gene":Please let me know if this does not meet your goal so that our support team can provide further assistance!