Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Bam quality vs read quality

    I have a cancer bam file and want to check its read qualities. I have two options in mind.
    1. Check bam quality through fastqc
    2. Convert the bam file into paired-end reads (in fastq) and check their quality in fastqc.
    Are both the processes equivalent?

  • #2
    Yes, because FastQC is a QC program. FastQC does not modify raw data. It is going to show you summary of the same Q-scores whether they come from the BAM or the fastq reads extracted from the BAM file.

    Comment


    • #3
      Sorry for the late followup to your reply. If that is the case, then why am I getting poorer quality when I convert the bam to 2 fastq files(read 1 and 2) whereas good quality when just checking the bam file as a whole?

      Comment


      • #4
        Probably, there is the problem with sorting. (check https://twitter.com/davisjmcc/status/931298649841188864 )

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Investigating the Gut Microbiome Through Diet and Spatial Biology
          by seqadmin




          The human gut contains trillions of microorganisms that impact digestion, immune functions, and overall health1. Despite major breakthroughs, we’re only beginning to understand the full extent of the microbiome’s influence on health and disease. Advances in next-generation sequencing and spatial biology have opened new windows into this complex environment, yet many questions remain. This article highlights two recent studies exploring how diet influences microbial...
          02-24-2025, 06:31 AM
        • seqadmin
          Quality Control Essentials for Next-Generation Sequencing Workflows
          by seqadmin




          Like all molecular biology applications, next-generation sequencing (NGS) workflows require diligent quality control (QC) measures to ensure accurate and reproducible results. Proper QC begins at nucleic acid extraction and continues all the way through to data analysis. This article outlines the key QC steps in an NGS workflow, along with the commonly used tools and techniques.

          Nucleic Acid Quality Control
          Preparing for NGS starts with isolating the...
          02-10-2025, 01:58 PM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 03-03-2025, 01:15 PM
        0 responses
        46 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-28-2025, 12:58 PM
        0 responses
        167 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-24-2025, 02:48 PM
        0 responses
        525 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 02-21-2025, 02:46 PM
        0 responses
        256 views
        0 likes
        Last Post seqadmin  
        Working...
        X