Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • Cutting bases from reads in a bam file - what other fields need to be changed?

    Hi,

    I'm writing a tool, which needs to cut bases from reads in a bam file. I'm not to familiar with the exact specifications of the bam format. So I'd like to ask what information I may to change to keep the bam correct.

    What I found so far:
    1. the qualities
    2. the CIGAR string
    3. the mate position, if bases from the start of mate were cut

    Anything else?

  • #2
    Probably all of the OPT flags (field 12). Official specifications are at:

    Comment


    • #3
      Trimming can also affect the mapping quality, and the bit flag might be incorrect if the shorter read becomes a multi-mapper. And, short of realignment, it will not be trivial to correct those values. That's why trimming is performed on FASTQs rather than BAMs.

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