Ensembl: How to convert gene names from GRCh37 to GRCh38

Question

[r.kalampaliki]

Hello, how could I convert the gene names from GRCh37 to GRCh38 ?

I have this GRCh37 list: 'SAA2', 'CXCL1', 'IL8', 'IGFBP5', 'ISG15'

and I would like to convert to this GRCh38 one: 'SAA2', 'CXCL1', 'CXCL8', 'IGFBP5', 'ISG15'

Notice that IL8 from GRCh37 list became CXCL8 in the GRCh38 list.

Thank you.

Answer 1

[Pierre Lindenbaum]

$ join -t $'\t' -11 -2 2 <(wget -q -O - "https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ensemblToGeneName.txt.gz" | gunzip -c |  sort -t $'\t' -k1,1 ) <( wget -q -O - "https://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/wgEncodeGencodeAttrsV40lift37.txt.gz" | gunzip -c | cut -f 2,5 | sed 's/\..*//' | sort -t $'\t' -k2,2) | cut -f 2- | grep -w -E '(SAA2|CXCL1|IL8|IGFBP5|ISG15)' | sort | uniq

CXCL1   CXCL1
IGFBP5  IGFBP5
IL8 CXCL8
SAA2    SAA2
SAA2-SAA4   SAA2-SAA4