problem with NCBI remap in genomic coordinates of SNP which arenot mapped · Biostar

This is a test version of Biostars. For the public version, visit https://www.biostars.org.

problem with NCBI remap in genomic coordinates of SNP which arenot mapped

Hi, I'm starting out new in bioinformatics. I'm trying to convert SNPs with genomic coordinates in ovis aries 3.1 assembly to oar_v4.0. I used map file (Oar_v 3.1) for making bed file and then remaped this file by NCBI Remap based on oar_ v4.0 The problem is that SNP on chr0 dosenot remaped by NCBI Remap dose any body know how can I get genomic coordinates of SNP in Oar_ v4.0 which are mapped on chromosome 0 in first assembly?

thanks a lot for any idea

snp remap cnbi

• 1,885 views • link

updated 9.5 years ago by Biostar

• written 9.5 years ago by mnosrati669 •

0 answers

No answers yet.

Log in to answer this question.

More posts like this

How to download Gene annotations (by Ensembl) track on NCBI Sequence Viewer 3.49.0
written 2.2 years ago by rahu •

I'm interested in an newer assembly of an organism available by NCBI but not by Ensembl. However, I still want to use the gene definitions …
Sheep reference genome remapping coordinates
written 2.3 years ago by valentinatsar •

Hi everyone, The latest sheep genome assemblies (Ramb_v1.0, Ramb_v2.0) are not available at liftover (https://genome.ucsc.edu/cgi-bin/hgLiftOver) while the NCBI Remap tool has been unfortunately retired. Do …
Find genes which are related to SNPs
written 3.4 years ago by hosin •

Hi Is there any chance to get SNPEff or some files which work like that in NCBI or other dataset? Actually I just want to …
VCF liftover for mouse strains
written 4.4 years ago by TheWonderer •

Hi there, I'm working on an allele skew project where we are utilizing two mouse strains. In order to perform some QC, we would like …
SNP coordinate systems in UCSC LiftOver (hg19), NCBI Remap (GRCh37(hg19)) and dbSNP (GRCh38(hg38))
written 10.3 years ago by curious •

Hi, I'm trying to understand the difference between the coordinate systems of different software: UCSC's `LiftOver`, `dbSNP` and `NCBI Remap`. I've a list of SNPs …
Search dbSNP for hg19 based coordinates
written 10.3 years ago by curious •

Hi, I'm starting out new in bioinformatics. I have couple of questions on searching dbSNP. 1. I'm searching (a list of rs# in [batch mode][1] …
creation of custom database in ANNOVAR for plant genome
written 10.7 years ago by Sathish •

<p>Hi everyone,</p> <p>How to create a custom database in ANNOVAR for plant genome (draft genome) using GFF3 file?</p> <p>I have downloaded corresponding genomic sequences and …
Inconsitency between Ensembl Assembly converter and UCSC LiftOver
written 11.9 years ago by Mo Sander •

I am using UCSC's liftover tool to port a number of genomic coordinates between hg19 and hg38. A tiny fraction of coordinates from hg19 does …
Inconsistencies When Trying To Identify Illumina Probes Containing A Snp
written 12.6 years ago by Rossella •

<p>Hi, I am trying to identify Illumina HT12v4 probes that contain a common SNP. I have downloaded the gene expression annotation file from Illumina.com and …
Retrieve Single Vcf From List Of Snp Rs#
written 13.5 years ago by Peixe

<p>Is there any straightforward way to retrieve in a single <strong>vcf</strong> file data for specified SNPs? In other words, I know how to slice <strong>1000Genomes</strong> …