[Feedback] Site Feedback: Rice NCBI dbSNPs

[Surya S]

Hi Marcela,

Thank you for your quick response!

Could you please send me the link to NCBI dbSNPs mapped to IRGSPv1?

Could you share with me the computational pipeline and tools that
Gramene used to import NCBI dbSNPs to IRGSPv1? I am using MSU7 build
for all my analysis and wondering how to integrate NCBI dbSNPs.

I noticed that the 400K SNPs from the Rice 3K genomes project in
Gramene ftp site is actually mapped to MSU7 build.

On Wed, Feb 25, 2015 at 3:26 PM, Marcela K. Monaco <mmonaco at cshl.edu> wrote:
> Dear Surya,
>
> The only SNPs from dbSNP that we have imported in Gramene & Ensembl Plants
> are those in dbSNP build 129.  All rice variants currently on display on our
> genome browser are mapped to IRGSPv1.  The 400K from the 3K genomes project
> were imported from OryzaSNP, converted to VCF and will appear in our
> upcoming Gramene build 45 in March.
> Hope this helps,
>
> Marcela
>
> On Wed, Feb 25, 2015 at 2:54 PM, feedback at gramene.org <feedback at gramene.org>
> wrote:
>>
>> URL         : http://www.gramene.org/
>>
>> Subject     : Site Feedback: Rice NCBI dbSNPs
>>
>> Name        : Surya
>>
>> Email       : nextgenseq.bioinfo at gmail.com
>>
>> Organization: UCLA
>>
>> Comments    :
>>
>> Hi,
>> I have been working with a strain of Rice and have mapped the reads to the
>> Nipponbare assembly v7.0 from MSU. I am looking for all annotated variants
>> from the various Rice cultivars studies (inc variants with indica spp) using
>> arrays and sequencing projects done so far. I looked into getting  NCBI
>> dbSNP although the VCF files they put out doesn't match the MSU Nipponbare
>> assembly. Perhaps, it was mapped to the RAP build.
>>
>> I realize Ensembl has a set of variants they derived from NCBI dbSNP
>> although these are also mapped to the IRGSP1.0 assembly GCA_000005425.2
>> http://plants.ensembl.org/Oryza_sativa/Info/Annotation#variation
>>
>> Is there an equivalent VCF file(s) for the Nipponbare assembly from MSU?
>>
>> I noticed you have the 400K core SNPs from the Rice 3K genomes project
>> mapped to the MSU7 build and wondering if you have mapped the NCBI dbSNP as
>> well.
>>
>> Thanks,
>> Surya
>>
>>
>> http://www.warelab.org/bugs/view.php?id=5124
>>
>>
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>
>