tool or database to convert Gene ID to genomic position
1
0
Entering edit mode
3.1 years ago
asalimih ▴ 60

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 • 1.0k views
ADD COMMENT
2
Entering edit mode
3.1 years ago
GenoMax 146k

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
ADD COMMENT
0
Entering edit mode

Thanks. how can I get the chromosome number?

ADD REPLY
1
Entering edit mode

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

ADD REPLY

Login before adding your answer.

Traffic: 820 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6