Ensembl: How to convert gene names from GRCh37 to GRCh38
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.
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$ 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
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