Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • bam files not sorted by samtools sort

    Hi,

    Could I please be adviced on the following problem. I have sam files generated from bismark. I converted it to bam file using samtools view and sorted it by coordinates using samtools sort. When I checked the header of both the sorted and unsorted bam files, they both stated the files are unsorted.

    I am unsure why this would be the case.

    Would anyone be able to shed light on this issue?

    Thanks

  • #2
    Which version of samtools did you use? Older versions never bothered to update the header (but still sorted the reads).

    Comment


    • #3
      I am using version 0.1.18. I am now certain that the files had not been sorted. I ran the files through our downstream analysis programs which threw an error indicating the flies were unsorted.

      Comment


      • #4
        The best test if a BAM file is sorted is to try "samtools index your_file.bam", if that works the file is coordinate sorted.

        Comment

        Latest Articles

        Collapse

        • seqadmin
          Current Approaches to Protein Sequencing
          by seqadmin


          Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...
          04-04-2024, 04:25 PM
        • seqadmin
          Strategies for Sequencing Challenging Samples
          by seqadmin


          Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...
          03-22-2024, 06:39 AM

        ad_right_rmr

        Collapse

        News

        Collapse

        Topics Statistics Last Post
        Started by seqadmin, 04-11-2024, 12:08 PM
        0 responses
        18 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 10:19 PM
        0 responses
        22 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-10-2024, 09:21 AM
        0 responses
        17 views
        0 likes
        Last Post seqadmin  
        Started by seqadmin, 04-04-2024, 09:00 AM
        0 responses
        49 views
        0 likes
        Last Post seqadmin  
        Working...
        X