tool or database to convert Gene ID to genomic position
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8 weeks ago
asalimih ▴ 30

Hello.
I have lots of Pseudogene IDs like LOC100431174 but none of the below methods worked for me to find their genomic position "offline". I need a table or package to do it offline without querying to a webpage.
methods I tried:
biomaRt: didn't have 100431174 in entrez id related annotations
genecode gtf files for hg38
ensembl gtf files for hg38
I can find them in ncbi like this but couldn't find this gene id in tools and dbs I mentioned. any help would be appreciated.

hg38 gene conversion id • 259 views
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8 weeks ago
GenoMax 108k

Since you want an offline solution, download gene2accession file from NCBI FTP site (Note: 2.1 G download).

Find the ID's you are looking for:

$ zgrep LOC100431174 gene2accession.gz 
9606    100431174       -       -       -       -       -       AC100850.2      19852141        39283   40290   +       -       -       -       LOC100431174
9606    100431174       INFERRED        -       -       -       -       NC_000008.11    568815590       15688632        15689637        -       Reference GRCh38.p13 Primary Assembly   -       -       LOC100431174
9606    100431174       INFERRED        -       -       -       -       NG_012141.2     325995142       153412  154417  -       -       -       -       LOC100431174
9606    100431174       INFERRED        -       -       -       -       NG_021238.2     350606306       100     1105    +       -       -       -       LOC100431174
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Thanks. how can I get the chromosome number?

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NC_000008 = chr8. Full table available here: https://www.ncbi.nlm.nih.gov/genome/?term=txid9606[Organism:noexp]

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