Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Time
  • Show
Clear All
new posts
Previous template Next
  • bioman1
    Member
    • May 2012
    • 80
    #1

    Jellyfish help

    Dear all,

    I am running jelly fish (jellyfish-2.1.1) for first time to estimate genome size. Although I followed manual, i am bit confused to estimate genome size. Below are my steps for kmer 27. Did I get correct genome size estimation. If I want to try different kmers to get best kmer & genome size how I do plotting? If any body have script to plot for different kmers and find best kmer and genome size, please share with me.


    jellyfish count -m 27 -s 100M -t 10 -C sample.filtered.fastq

    jellyfish histo -f mer_counts.jf > histogram.txt

    jellyfish stats -v -o stats.txt mer_counts.jf
    less stats.txt
    Unique: 659211049
    Distinct: 2297173537
    Total: 31359408599
    Max_count: 16054234
    (END)


    less histogram.txt (first 10 rows)
    0 0
    1 659211049
    2 94535838
    3 109738065
    4 125218564
    5 126564348
    6 117188987
    7 103591231
    8 90823407
    9 80950377
    10 74112334

    Genome size estimation= totalnumber of distant kmers - distinct error kmers
    Genome size estimation=31359408599 - 2297173537 = 31130235062
    Last edited by bioman1; 04-02-2014, 11:58 AM.
    Tags: genomesize, jellyfish
    Previous template Next

    Latest Articles

    Collapse
    • SEQadmin2
      Multiomic Liquid Biopsy: What DNA/RNA Panels Reveal That DNA Alone Can’t
      by SEQadmin2



      Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?

      Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating      ...
      10-14-2026, 09:55 AM
    • SEQadmin2
      New Genomics Technologies Take Aim at Long-Standing Limits
      by SEQadmin2


      Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.

      We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing      ...
      09-28-2026, 10:25 AM
    View All

    ad_right_rmr

    Collapse

    News

    Collapse
    Topics Statistics Last Post
    Exeter-Led Study Maps What an Average Human Genome Looks Like by SEQadmin2
    Started by SEQadmin2, Yesterday, 11:13 AM
    0 responses
    16 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    Yesterday, 11:13 AM  
    Long-Read Sequencing Uncovers Cancer Mutations Conventional Testing Missed by SEQadmin2
    Started by SEQadmin2, Yesterday, 10:48 AM
    0 responses
    17 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    Yesterday, 10:48 AM  
    Mayo Clinic-Led Study Detects DNA Mutations Across Noncancerous Tissues by SEQadmin2
    Started by SEQadmin2, 10-15-2026, 10:52 AM
    0 responses
    35 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    10-15-2026, 10:52 AM  
    Study Finds Chromatin Motion Holds Steady Until Cells Face Stress by SEQadmin2
    Started by SEQadmin2, 10-14-2026, 05:39 AM
    0 responses
    42 views
    0 reactions
    		 Last Post SEQadmin2
    by SEQadmin2
    10-14-2026, 05:39 AM  
    View All
    Working...