Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Extracting alternate loci from fasta genome

    Dear all,

    I downloaded full reference fasta genomes for hg19, mm9 and mm10 from gencode. They include reference chromosomes, scaffolds, assembly patches and haplotypes.
    For a specific purpose, I want to remove haplotypes.
    I did not manage to find a description of the nomenclature used for the contigs in fasta file.
    In the hg19 reference genome I use, there are 297 contigs. One can see for example:
    >chr1 1
    >chr2 2
    ...
    >chrM MT
    >GL877870.2 HG1007_PATCH
    >GL877872.1 HG1032_PATCH
    ...
    >GL383545.1 HSCHR10_1_CTG2 <- is it an "unlocalized sequence" ?
    >GL383546.1 HSCHR10_1_CTG5
    ...
    >GL000191.1 GL000191.1
    >hg19GL000192.1 GL000192.1
    I would like to know how many of them are haplotypes and which ones are they.
    Is there a way to get this information?

    Thank you in advance for your help.

  • #2
    If it can help someone in the future, we can get this type of information on NCBI: ftp://ftp.ncbi.nlm.nih.gov/genomes/g...ate_mammalian/
    In *_report.txt files, for each contigs, there is assembled-molecule / unlocalized-scaffold / unplaced-scaffold / novel-patch / fix-patch or alt-scaffold.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Strategies for Sequencing Challenging Samples
      by seqadmin


      Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
      03-22-2024, 06:39 AM
    • seqadmin
      Techniques and Challenges in Conservation Genomics
      by seqadmin



      The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

      Avian Conservation
      Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
      03-08-2024, 10:41 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, Yesterday, 06:37 PM
    0 responses
    12 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, Yesterday, 06:07 PM
    0 responses
    10 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-22-2024, 10:03 AM
    0 responses
    52 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 03-21-2024, 07:32 AM
    0 responses
    68 views
    0 likes
    Last Post seqadmin  
    Working...
    X