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
          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, 07-19-2024, 07:20 AM
        0 responses
        25 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-16-2024, 05:49 AM
        0 responses
        41 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-15-2024, 06:53 AM
        0 responses
        46 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 07-10-2024, 07:30 AM
        0 responses
        42 views
        0 likes
        Last Post seqadmin  
        Working...
        X