Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Starting the analysis of 454 data

    Hi all,

    I am newbie and I will have to start the analysis of 454 Roche data very soon.
    I was wondering if you have any recommendation about the analysis.

    The fist step will be to map the reads to the genome (here Arabidopsis thaliana)
    For that, I am still not sure of which tool to use.. Eland or MaQ simply BLAST??

    I will be happy to have any suggestion from the people who are already into this.

    Thanks a lot,
    Naira

  • #2
    For GS-FLX reads you need an alignment program that can handle the 250bp / 400bp reads generated by the GS-FLX. Blast is probably only good enough for a first estimte of where a read might align (possibly several positons) and to give an estimate of how many reads do not align. Even if you do a Smith-Waterman alignment of the regions around every Blast hit (+/-300bp, for example) it will only take a weekend to map the reads from a flx run (depending on the computer). That is the easy part. The hard part is designing and implementing a database that can help with the analysis A database and genome browser to store the reads and positions as well as quality metrics (things like number of mismatches) is probably a good idea. If need be, you can exclude things that are trivial. For example, if you are looking for SNPs, you don't need to keep reads that are 100% identical. Of course the structure will depend on the questions you are asking.
    Gook Luck

    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, Yesterday, 11:09 AM
    0 responses
    16 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-19-2024, 07:20 AM
    0 responses
    148 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-16-2024, 05:49 AM
    0 responses
    124 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-15-2024, 06:53 AM
    0 responses
    111 views
    0 likes
    Last Post seqadmin  
    Working...
    X