Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • find areas of very low and extra high coverage in NGS data

    Are there any tools that can report all areas of very low coverage or areas of high coverage in NGS data?

  • #2
    I've written some custom code to programatically do this, but it only works on a few assembly formats (don't have time or funding to add more formats yet). But several assembler programs have ways to output the coverage levels of the contigs. It would then be up to you to parse that output and find any locations that are below or above your thresholds.

    Comment


    • #3
      A commonly used method is to map all your reads to contigs using bowtie2/bwa mem/bwa and calculate the coverage with samtools or bedtools.

      Comment


      • #4
        Originally posted by willMD View Post
        Are there any tools that can report all areas of very low coverage or areas of high coverage in NGS data?
        Can you give us some more information? What type of data do you have? Have you mapped reads to a reference yet?

        If you do have a bam file of aligned reads to a reference sequence then you will be able to generate a plot of the per-base coverage of the reference sequence using bedtools genomeCoveragebed.

        Comment


        • #5
          Human whole genome data aligned to hg19 in bam file. Thanks. I'll look at bedtools.

          Comment

          Latest Articles

          Collapse

          • seqadmin
            Best Practices for Single-Cell Sequencing Analysis
            by seqadmin



            While isolating and preparing single cells for sequencing was historically the bottleneck, recent technological advancements have shifted the challenge to data analysis. This highlights the rapidly evolving nature of single-cell sequencing. The inherent complexity of single-cell analysis has intensified with the surge in data volume and the incorporation of diverse and more complex datasets. This article explores the challenges in analysis, examines common pitfalls, offers...
            06-06-2024, 07:15 AM
          • seqadmin
            Latest Developments in Precision Medicine
            by seqadmin



            Technological advances have led to drastic improvements in the field of precision medicine, enabling more personalized approaches to treatment. This article explores four leading groups that are overcoming many of the challenges of genomic profiling and precision medicine through their innovative platforms and technologies.

            Somatic Genomics
            “We have such a tremendous amount of genetic diversity that exists within each of us, and not just between us as individuals,”...
            05-24-2024, 01:16 PM

          ad_right_rmr

          Collapse

          News

          Collapse

          Topics Statistics Last Post
          Started by seqadmin, Yesterday, 07:24 AM
          0 responses
          10 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-13-2024, 08:58 AM
          0 responses
          11 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-12-2024, 02:20 PM
          0 responses
          16 views
          0 likes
          Last Post seqadmin  
          Started by seqadmin, 06-07-2024, 06:58 AM
          0 responses
          184 views
          0 likes
          Last Post seqadmin  
          Working...
          X