Which Genes Are Contained In The Alternate Reference Loci In Hg38?

Question

[Giovanni M Dall'Olio]

The most recent versions of the human genome assembly (e.g. hg38 and GRch37) contain a new feature, called alternate reference loci.

How can I see which genes are included in these regions? I would guess that these correspond mostly to HLA and olfactory regions.

Answer 1

[Pierre Lindenbaum]

try this ?

$ curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz" | gunzip -c | awk -F ' ' '$3 ~ /alt$/' | cut -f 3,13 | uniq 

chr10_GL383545v1_alt    PTCHD3
chr10_GL383546v1_alt    OR13A1
chr10_GL383546v1_alt    ALOX5
chr10_GL383546v1_alt    MARCH8
chr10_KI270825v1_alt    DLG5
chr10_KI270825v1_alt    DLG5-AS1
chr11_JH159136v1_alt    OR5T2
chr11_JH159136v1_alt    OR5T3
chr11_JH159136v1_alt    OR5T1
chr11_JH159136v1_alt    OR8H1
(..)

[Giovanni M Dall'Olio]

Thanks! I could not find the table. You should also add "cut -f2 | sort| uniq | wc -l" because some genes are repeated (they appear in more than one alternate locus). The answer I get now is 1039.

[zx8754]

sort -u is slightly faster and less keystroke than sort | uniq Sort & uniq in Linux shell