Pseudogenes list

[Hani Choudhry]

Dear UCSC,

How can I download the human pseudogenes list (HG19)?

Regards,

Hani

[Hiram Clawson]

You can use the "Yale Pseudo60" track: "Yale Pseudogenes based on Ensembl Release 60"
http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=pseudoYale60

--Hiram

[Pauline Fujita]

Hello again Hani,

You might also want to check out the GENCODE pseudogenes tracks. You
can read about them on the description page for GENCODE v12 here:

http://www.genome.ucsc.edu/cgi-bin/hgTrackUi?c=chr21&g=wgEncodeGencodeV12

In particular if the GENCODE Pseudogenes track is useful for you, it
can be obtained using our Table Browser tool here:

http://www.genome.ucsc.edu/cgi-bin/hgTables

Once there select:

group: Genes and Gene Prediction Tracks
track: GENCODE Genes v12
table: Pseudogenes (wgEncodeGencodePseudoGeneV12)

region: genome

output format: "all fields...", or if you want to restrict output to
only the pseudogene names you can choose "selected fields from primary
and related tables" and select the appropriate fields from the
underlying table there.

Similarly, if you find the "GENCODE 2-way Pseudogenes" track is more
appropriate you can follow the analogous steps above.

If you have further questions please feel free to contact the mailing
list again at gen...@soe.ucsc.edu.

Best regards,

Pauline Fujita
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu

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