Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • gene annotation in sequenced cancer genome

    Hi all,

    I am dealing with ChIP-seq data for a small lung cancer sample. The genomic sequences of this cancer sample is available in this paper: "A small-cell lung cancer genome with complex signatures of tobacco exposure". We are trying to build a specific reference genome based on the whole genome sequences provided in this paper and map our ChIP-seq data back to this specific reference genome.
    My problem is that the gene annotation files like GTF files will be very different for this specific reference genome and common reference genome (Hg19), because of the somatic variation (insertions, deletions, rearrangements) in this cancer genome. The coordinates for transcripts will change a lot. Is there a software of program to solve this problem?
    Something like by providing hg19 GTF files and information for all somatic variations as listed in this link, it can output a gene annotation file for this specific cancer reference genome.
    or if not, could someone give a clue about how to cleverly do that?

    Thanks a lot!

  • #2
    If this is human (I'm assuming it's not one of these fellows : http://www.holytaco.com/25-smoking-monkeys/ ), you can get the sequences for the human genes from genbak/ncbi/entrez and blat them against your custom(?) genome. This is fairly easy to set up if you know how to script and process a big data set. It is still a big job in terms of horsepower needed but easily paralleizeable if you have access to many computers. You may need to fine tune the blat alignment parameters and filter the results for good hits. The results will give you the coordinates for the genes.

    Comment

    Latest Articles

    Collapse

    • seqadmin
      Exploring the Dynamics of the Tumor Microenvironment
      by seqadmin




      The complexity of cancer is clearly demonstrated in the diverse ecosystem of the tumor microenvironment (TME). The TME is made up of numerous cell types and its development begins with the changes that happen during oncogenesis. “Genomic mutations, copy number changes, epigenetic alterations, and alternative gene expression occur to varying degrees within the affected tumor cells,” explained Andrea O’Hara, Ph.D., Strategic Technical Specialist at Azenta. “As...
      07-08-2024, 03:19 PM
    • seqadmin
      Exploring Human Diversity Through Large-Scale Omics
      by seqadmin


      In 2003, researchers from the Human Genome Project (HGP) announced the most comprehensive genome to date1. Although the genome wasn’t fully completed until nearly 20 years later2, numerous large-scale projects, such as the International HapMap Project and 1000 Genomes Project, continued the HGP's work, capturing extensive variation and genomic diversity within humans. Recently, newer initiatives have significantly increased in scale and expanded beyond genomics, offering a more detailed...
      06-25-2024, 06:43 AM

    ad_right_rmr

    Collapse

    News

    Collapse

    Topics Statistics Last Post
    Started by seqadmin, 07-19-2024, 07:20 AM
    0 responses
    40 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-16-2024, 05:49 AM
    0 responses
    52 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-15-2024, 06:53 AM
    0 responses
    63 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-10-2024, 07:30 AM
    0 responses
    43 views
    0 likes
    Last Post seqadmin  
    Working...
    X