Question: finding directly the snp ids for the variants of each gene
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gravatar for jananiinfo14
10 months ago by
jananiinfo140 wrote:

How to find directly the snp ids for the variants of each gene? thanks in advance

variants dbsnp omim • 373 views
ADD COMMENTlink modified 10 months ago by Pierre Lindenbaum112k • written 10 months ago by jananiinfo140

Hello jananiinfo14!

We believe that this post does not fit the main topic of this site.

Insufficient information to get an answer, elaborate if you want help.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLYlink written 10 months ago by WouterDeCoster32k
1

I think that's a little unfair. Yes, this is a naive question, but many people starting out their bioinformatics analyses are very naive and lack support in this area in their home institutes. We may be their only support.

(Also, it's an opportunity for me to suggest a newbie tries Ensembl. Not self-interested at all.)

ADD REPLYlink modified 10 months ago • written 10 months ago by Emily_Ensembl15k

That's a valid point and concern, and definitely, we should stay supportive of those people. But in addition to being naive, this type of questions is also often a big waste of time when we try to drill down to find out what the OP truly wants to know. My first interpretation was that the OP has a vcf file and wants to annotate these with dbSNP id's, but your answer is also a possibility. With just a bit more effort on the side of the OP, this could be far easier and save a ton of effort for the community.

ADD REPLYlink written 10 months ago by WouterDeCoster32k

In that case I would comment with a question, but I wouldn't close it. When you close it you're really shutting down the conversation and making the OP feel like they can't ask naive questions, just asking a question invites them to engage.

ADD REPLYlink written 10 months ago by Emily_Ensembl15k

You are right - I will be more patient. I'm glad that moderatorship here is an itself-correcting system.

ADD REPLYlink written 10 months ago by WouterDeCoster32k
0
gravatar for Emily_Ensembl
10 months ago by
Emily_Ensembl15k
EMBL-EBI
Emily_Ensembl15k wrote:

An easy way to do this is with Ensembl. Search for your gene name then go to Variant Table in the left hand menu to get a list of all the variants in the gene.

ADD COMMENTlink written 10 months ago by Emily_Ensembl15k
0
gravatar for Pierre Lindenbaum
10 months ago by
France/Nantes/Institut du Thorax - INSERM UMR1087
Pierre Lindenbaum112k wrote:

using UCSC/mysql:

$ mysql --user=genome --host=genome-mysql.soe.ucsc.edu -A -D hg19 -e 'select distinct S.name,R.name2 from snp150 as S, refGene as R where R.chrom=S.chrom and NOT(S.chromEnd<=R.txStart OR S.chromStart>=R.txEnd) and R.name2="NOTCH2" '
+-------------+--------+
| name        | name2  |
+-------------+--------+
| rs782287146 | NOTCH2 |
| rs150344945 | NOTCH2 |
| rs782430685 | NOTCH2 |
| rs191431654 | NOTCH2 |
| rs759289101 | NOTCH2 |
| rs868973669 | NOTCH2 |
| rs782330458 | NOTCH2 |
| rs782630792 | NOTCH2 |
| rs782609720 | NOTCH2 |
| rs2453056   | NOTCH2 |
(...)
ADD COMMENTlink written 10 months ago by Pierre Lindenbaum112k
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