Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • convert hg19 to hg18, chr mismatch

    when I convert hg19 to hg18, some positions from chr3 in hg19 are matched to chr2 in hg18. e.g. chr2:5144329 in hg19 are matched to chr3:165545129
    Does anyone know why?

  • #2
    Interesting; I have not seen that. It looks like portions of the chromosomes were rearranged between the different assemblies. If you download the liftOver hg19 to hg18 chain file and type in
    Code:
    grep 'chr 2' [hg19_to_hg18_chainfile] | grep 'chr 3' | less
    you will see:

    Code:
    chain 25982 chr2 243199373 + 16340754 16341023 chr3 199501827 - 118072788 118073057 6523537
    chain 4737 chr2 243199373 + 5145834 5145884 chr3 199501827 - 155139362 155139412 33407240
    chain 4607 chr2 243199373 + 5145066 5145350 chr3 199501827 + 191348934 191349218 1967131
    chain 2538 chr2 243199373 + 16338477 16338504 chr3 199501827 - 154040818 154040845 35425972
    chain 1237 chr2 243199373 + 5143151 5144336 chr3 199501827 - 33955506 33956705 3724972
    The position you listed would fall within the last line.

    Comment


    • #3
      have you tried to look at the sequence to see if its the same?

      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
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      51 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X