How to convert chromosome locations to gene symbols?
Hi.
I wonder how to convert chromosome locations to gene symbols.
An example of chromosome locations name is 'chr1: 44959708-45072070'. There are many chromosome locations.
I want the chromosome location names to gene symbols.
Should I use 'biomaRt' package? If I need to use the 'biomaRt' package, how can I change the example chromosome location name to a gene symbol?
Please help me.
2 answers
Here's an R solution using biomaRt
To Get All Genes Within A Genomic Region
A solution:
wget -q -O - "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_43/gencode.v43.annotation.gtf.gz" |\
gunzip -c |\
awk -F '\t' '($3=="gene" && $1=="chr1" && !(int($4)>45072070 || int($5)<44959708))' | cut -f 9 |\
tr ";" "\n" | grep -Fw gene_name | cut -d '"' -f 2 | sort | uniq
EIF2B3
HECTD3
MRPS17P1
OSTCP5
PPIAP35
UROD
ZSWIM5
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Pierre Lindenbaum
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