How to get new SNP coordinate with new reference genome

Hi, I have a list of SNPs coordinates corresponding to IRGSP 4.0 reference genome, how can I get the right coordinates of these SNPs in another rice reference genome such as IRGSP 1.0 reference genome? Thank you very much!

Best, Aifu.

snp coordinate reference

• 777 views • link

written 7.2 years ago by afli

duplicate: Converting Genome Coordinates From One Genome Version To Another (Ucsc Liftover, Ncbi Remap, Ensembl Api)

• 0 views • link

written 7.2 years ago by Pierre Lindenbaum

Thank you for your kindly suggestion!

• 0 views • link

written 7.2 years ago by afli

0 answers

No answers yet.

More posts like this

How to compare and complement the missing gene and feature in gff3 file base on available gff3 refe…
written 1.7 years ago by Sony Nguyen •

Hi everyone, I am doing annotation for rice pangenome. The pangenome was created based on an iterative mapping and assembly approach. The pangenome including IRGSP-1.0 …
chromosome location to gene name and aa change
written 3.2 years ago by Zi •

Hi, I have just found an annotation metric, which contains data in these columns, ``` CHROM : chromosome POS : position REF : reference nucleotide …
very low Bowtie2 mapping rate
written 7.8 years ago by afli

Dear all, I download a single end reads fastq file from a published article in 2012, when I mapped these reads to the reference genome …
How to identify differential expressed genes if the normalization assumptions are violated
written 7.8 years ago by afli

Hi, I do the DESeq2 analysis of RNA-seq samples from two different tissues, each with 3 replicates, and both PCA or sample correlation heatmap results …
Compare expression of one group to the mean of others using DESeq2
written 7.8 years ago by afli

Hi, I want to compare one condition to the mean of the other two conditions, sample data are as follows(the sample data is borrowed from …
Kallisto and homologous genes expression
written 8.0 years ago by afli

Hi, I met some trouble when using kallisto to analyse homologous genes expression. In my case, sample1 and sample2 are two varieties with very similar …
How to evaluate the similarity of genes between two sample
written 8.0 years ago by afli

Hi, everyone，there are many methods to see whether two sets of data are different. For example, if we have three replicates of one gene between …
liftover between close species
written 8.8 years ago by tim.ivanov.92 •

I have 2 coordinates on the reference genome, and i want to find corresponding nucleotide sequences of this region on a list a close related …
Where to find TIGR reference genome data and version conversion with IRGSP
written 9.1 years ago by jesselee516

Hi, all. I am looking for **Rice(Oryza sativa) TIGR5 reference genome fasta data** and **corresponding detail annotation**. But I notice that TIGR project is closed …
Substituting Snps On Reference Genome Assemblies
written 13.2 years ago by Sakti

<p>Hi again guys!</p> <p>So this time with a new question. I have a list of variant calls (basically, SNPs) for a mouse genome sample. SNP …