Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • GRCh37: how to use lates patches

    I would like to know how to assemble human refefence genome GRCh37 from individual chromosome files and latest patches.

    This is ensembl's ftp site which lists >300 fasta files.
    ftp://ftp.ensembl.org/pub/release-67...o_sapiens/dna/

    For primary assembly, one might simply concatenate chromosome 1, 2, ..., X, and Y. However, X and Y chromosomes share pseudoautosomal region (PAR) as README points out. I could just leave out Y chromosome since I work on K562 cells, but otherwise what am I supposed to do? There is a big file called toplevel.fa which appears to have PAR sequenes masked, but does it contain all chromosomes and patches? README does not say anything about its content.

    There seem to be two kinds of patches: fixes and novel additions. How are these patches correctly incorporated into the primary assembly? Is there a utility software to handle this? Or are patches treated as separate entities (e.g. as PATCH_xxx instead of being integrated into chromosome proper)?

    Thank you for your very kind help.
    Last edited by yujiro; 07-13-2012, 03:20 AM.

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