A question about pseudogene

[Liu,Yang]

Dear Sir or Madam,

 

This is Yang Liu, a data scientist from MD Anderson cancer center. I am working on a project that we need to delete the pseudogenes from our DGE result. I refer to your website http://genome.ucsc.edu/cgi-bin/hgTables and found that the currently available pseudogene list is generated based on the GRCh38/hg38). However, my mRNA data was referenced to hg19. I am wondering if the pseudogene list referenced to hg19 is available from you now?

 

I am looking forward to your response. Your time will be highly appreciated.

 

Best regards,

 

Yang

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[Jairo Navarro Gonzalez]

Hello,

Thank you for using the UCSC Genome Browser and sending your inquiry.

You can use the NCBI RefSeq track to get a list of pseudogenes for the hg19 genome assembly. To generate the list, you will have to create a filter on the Table Browser. You can follow these steps to get all pseudogenes on hg19:

1. Configure the Table Browser

clade: Mammal
organism: Human
assembly: Feb. 2009 (GRCh37/hg19)
group: Genes and Gene Predictions
track: GENCODE V43lift37
table: Pseudogenes (wgEncodeGencodePseudoGeneV43lift37)
region: genome

2. Create a filter

Next to the filter setting, click the create button, and you will be taken to a new page. Scrolling down to the bottom, select the wgEncodeGencodeAttrsV43lift37 table and click allow filtering using fields in checked tables.

You will need to create the filter for the transcriptClass field on the wgEncodeGencodeAttrsV43lift37 table. The filter should be set as:

transcriptClass does match pseudo

Next, click submit

3. Get output

After creating the filter, you can configure the output settings. For example, you could create a BED file from the results by changing the output format drop-down menu or download the data to a file by adding an output filename.

Once you have configured the output settings, click the get output button. Depending on your output choices, you will see the data in your web browser or begin downloading a file.

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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