User: deepak.k.choubey

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New User
Location:
Canada
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20 hours ago
Joined:
3 years, 4 months ago
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d***************@gmail.com

Posts by deepak.k.choubey

<prev • 28 results • page 1 of 3 • next >
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SNP associated disease
... Dear All, Can someone please help me to know how to find if a SNP like "rs780819072" is associated with a disease or not? Thanks much! DK ...
snp written 2 days ago by deepak.k.choubey10 • updated 2 days ago by Kevin Blighe3.2k
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Ensembl and Aceview - difference in the UTR sequence
... Dear All, Can someone please help me to understand why is there difference in the sequences length (below) for the 5' UTR of BRCA2 from two sources "Aceview" and "Ensembl"? and which one is the reasonable to be used for any analysis to be done? From "Aceview": https://www.ncbi.nlm.nih.gov/ieb/rese ...
genome sequence written 14 days ago by deepak.k.choubey10
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Comment: C: Reference and mutant allele of a SNP rsID
... Thanks much! But, am a little lost since there is a lot of information in the link. If you could please guide me to what information I should be looking in the link, I would really appreciate. I do see "rsnumber ID" like this: /variation/human/rs56116432?content-type=application/json "na ...
written 16 days ago by deepak.k.choubey10
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Comment: C: Reference and mutant allele of a SNP rsID
... thanks! but, I want to get this information locally, as I have to do this for 1000s of rsIDS. Can you tell me how can I get this information locally using any tool or linux command or script? ...
written 17 days ago by deepak.k.choubey10
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Reference and mutant allele of a SNP rsID
... Dear All, Can someone please tell me how to get the reference and the mutant allele of a rsID; like for this rsID "rs80357307" what is the reference allele and the mutant allele? Thanks much! ...
snp written 17 days ago by deepak.k.choubey10 • updated 16 days ago by Ben_Ensembl470
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Comment: C: Extract the region and mutant SNP allele
... Thanks! Can you please tell me a reliable source from where I can download the chromosome fasta files for bedtools? ...
written 17 days ago by deepak.k.choubey10
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Comment: C: Extract the region and mutant SNP allele
... Thanks! I guess, I need to download the chromosome fasta file locally to run bedtools? Can it be done without downloading the chromosome fasta file locally? ...
written 17 days ago by deepak.k.choubey10
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Extract the region and mutant SNP allele
... Dear All, I have data related to the SNPs like this: 1) The chromosome region for the 5' and 3' UTRs obtained from Ensembl. For example, in this example below the 5' and 3' UTRs are from chromosome 17 and their respective regions are also shown. 5'-UTR: 17:43124097-43124115 3'-UTR: 1 ...
snp written 17 days ago by deepak.k.choubey10
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Comment: C: SNP position in UTRs
... Thanks Fin! :-) The program gives the rsIDs output of the UTRs. I was asking about getting the 5' and 3' UTR sequence between these regions: 5'-UTR: 17:43124097-43124115 3'-UTR: 17:43044295-43045677 like this below: (Could you please share how this could be done?) >NM_007299. ...
written 23 days ago by deepak.k.choubey10
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Comment: C: SNP position in UTRs
... what you get back from the REST-API is in JSON format. Most commonly used programming languages can parse this format very easyly. Which one dou you want to use? Thanks Fin! I would like to use Bash/shell to extract the regions. Could you please tell me how this complete procedure can be automa ...
written 24 days ago by deepak.k.choubey10

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