Number of pseudogenes in NCBI GRCh37

Question

[Joey]

I downloaded the NCBI GRCh37 gene list from https://bitbucket.org/baderlab/fast/downloads.

What is the best way to find out how many are pseudogenes in this list? I tried Biomart but I wasn't able to do a full merge.

Thanks,

-Joey

Answer 1

[Ashutosh Pandey]

I can't help you with your list but if you just need to get an idea then you can use UCSC table browser:

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

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -D hg38 -e ' select distinct name,name2 from wgEncodeGencodePseudoGeneV19'

[JMMM]

Let me slightly update this answer with recent information from GENCODE V31 (July 2019, http://genome.ucsc.edu/goldenpath/newsarch.html ) which contains 18.536 annotated pseudogenes (not including polymorphic pseudogenes, according to documentation)

• group: Genes and Gene Prediction Tracks
• track: GENCODE Genes v12
• table: Pseudogenes (wgEncodeGencodePseudoGeneV31lift37)
• output format: select fields from primary and related tables

Specify output file name and check chrom, cdsStart, cdsEnd and name2 in the required fields to get the desired .bed file