Seqanswers Leaderboard Ad

Collapse

Announcement

Collapse
No announcement yet.
X
 
  • Filter
  • Time
  • Show
Clear All
new posts

  • Variant format conversion to genome coordinates

    Hello everyone,

    My name is Krishna, and I am currently working as a project student in the field of Clinical Genetics, specifically the rare variant disease study of patient exome and whole-genome samples.

    I am attempting to convert various representation formats such as Gene symbol, RefSeq ids, HGVSc, HGVSp, dbSNP IDs, and ENST IDs, along with amino acid or nucleotide changes, into their corresponding genomic coordinates. This conversion will aid in better understanding the variations. An example is provided below for more clarity:

    I have a variation that can be represented in multiple ways, as shown below:

    rs1639927683
    OR4F5.M1T
    OR4F5.Met1Thr
    OR4F5:c.2T>C
    NM_001005484.M1T
    NM_001005484.Met1Thr
    NM_001005484:c.2T>C
    NP_001005484.M1T
    NP_001005484.Met1Thr
    ENST00000641515:c.2T>C

    For all the given formats, the corresponding genomic coordinates are 1-65566-T-C.

    Q. How can I convert any format of variation to its corresponding genomic coordinates, as shown in the example above?

    I have used Ensembl's Variant Recoder, but it operates in online mode, which is time-consuming, especially considering I have multiple variations in different formats.

    Can anyone please suggest a more efficient approach to tackle this situation which is preferably offline mode with all the databases?

    Thank you very much in advance.

Latest Articles

Collapse

  • seqadmin
    Recent Advances in Sequencing Analysis Tools
    by seqadmin


    The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...
    05-06-2024, 07:48 AM
  • seqadmin
    Essential Discoveries and Tools in Epitranscriptomics
    by seqadmin




    The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...
    04-22-2024, 07:01 AM

ad_right_rmr

Collapse

News

Collapse

Topics Statistics Last Post
Started by seqadmin, 05-14-2024, 07:03 AM
0 responses
23 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-10-2024, 06:35 AM
0 responses
44 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-09-2024, 02:46 PM
0 responses
57 views
0 likes
Last Post seqadmin  
Started by seqadmin, 05-07-2024, 06:57 AM
0 responses
44 views
0 likes
Last Post seqadmin  
Working...
X