Unconfigured Ad

Collapse
X
Collapse
 
  • Page of 1
  • Filter
  • Time
  • Show
Clear All
new posts
Previous template Next
  • tahamasoodi
    Success
    • May 2012
    • 130
    #1

    Sequencing statistics

    Hi,

    May I know how can we calculate the following from whole genome/exome data?

    Reads mapped to the human genome
    Reads mapped to the target regions (exome)
    Coverage of target regions at 1x
    Coverage of target regions at 10x
    Coverage of target regions at 50x
    Thanks,
    Tags: None
  • aaronh
    Member
    • Sep 2008
    • 46
    #2
    GATK's DepthOfCoverage will do this.

    Comment

    • tahamasoodi
      Success
      • May 2012
      • 130
      #3
      Thanks, but it is giving results by position wise. I need the overall average. Is there anyway to do that in GATK.
      Thanks,

      Comment

      • aaronh
        Member
        • Sep 2008
        • 46
        #4
        One of the files it generates: SAMPLE_NAME.sample_summary has that. The sample_cumulative_coverage_proportions file will tell you how much of the genome is covered by some X.

        Comment

        • tahamasoodi
          Success
          • May 2012
          • 130
          #5
          Ok, it is running now and i'm waiting for the results. Will it tell anything on the number of on target genotypes at a particular X?
          Thanks,

          Comment

          Previous template Next

          Latest Articles

          Collapse
          • SEQadmin2
            Advanced Sequencing Platforms Tackle Neuroscience’s Toughest Genomics Problems
            by SEQadmin2



            Genomics studies in neuroscience face a special challenge due to the brain’s complexity and scarcity of samples. Mapping changes in cell type and state using conventional next-generation sequencing methods remains challenging. Advances in technologies like single-cell sequencing, spatial transcriptomics, and long-read sequencing have opened the door to deeper studies of the brain and diseases like Alzheimer’s, amyotrophic lateral sclerosis (ALS), and schizophrenia.
            ...
            07-09-2026, 11:10 AM
          • SEQadmin2
            Cancer Drug Resistance: The Lingering Barrier to Rising Survival
            by SEQadmin2



            Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

            There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
            07-08-2026, 05:17 AM
          • GATTACAT
            Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing
            by GATTACAT
            Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
            07-01-2026, 11:43 AM
          View All

          ad_right_rmr

          Collapse

          News

          Collapse
          Topics Statistics Last Post
          UC San Diego Bioengineers Map Gene Function in Human Stem Cells by SEQadmin2
          Started by SEQadmin2, 07-13-2026, 10:26 AM
          0 responses
          24 views
          0 reactions
          		 Last Post SEQadmin2
          by SEQadmin2
          07-13-2026, 10:26 AM  
          New Analysis Splits Leukemia Into 16 Epigenomic Subgroups by SEQadmin2
          Started by SEQadmin2, 07-09-2026, 10:04 AM
          0 responses
          34 views
          0 reactions
          		 Last Post SEQadmin2
          by SEQadmin2
          07-09-2026, 10:04 AM  
          Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2
          Started by SEQadmin2, 07-08-2026, 10:08 AM
          0 responses
          21 views
          0 reactions
          		 Last Post SEQadmin2
          by SEQadmin2
          07-08-2026, 10:08 AM  
          Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2
          Started by SEQadmin2, 07-07-2026, 11:05 AM
          0 responses
          34 views
          0 reactions
          		 Last Post SEQadmin2
          by SEQadmin2
          07-07-2026, 11:05 AM  
          View All
          Working...