Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • samtools vs. bedtools

    Hi all,

    I use samtools (depth) and bedtools (coverageBed -d) to calculate coverage for a given bedfile, the results are different

    In the following dataset, the first three columns are generated by samtools, the rest are generated by bedtools. At most of the positions (>65%), cov1=cov2, at some positions the differences are huge. For example, at chr1:237433808, cov1 =522 (samtools), while cov2 = 649 (bedtools).

    Ant explanation?

    chrs posi cov1 start ends count cov2
    chr1 237433798 647 237433797 237433916 1 649
    chr1 237433799 647 237433797 237433916 2 649
    chr1 237433800 647 237433797 237433916 3 648
    chr1 237433808 522 237433797 237433916 11 649
    chr1 237433826 653 237433797 237433916 29 654
    chr1 237433828 653 237433797 237433916 31 654
    chr1 237433829 654 237433797 237433916 32 655
    chr1 237433830 654 237433797 237433916 33 655
    chr1 237433831 654 237433797 237433916 34 655
    chr1 237433833 654 237433797 237433916 36 655

  • #2
    While you mention "a given bedfile", I suppose you use a BAM as the original input (possibly converted for coverageBed) in both cases, right? Since you seem to have consistently higher counts with BEDTools, this could be due a different definition of coverage in the case of splices (or other non-matching CIGAR operations) of read alignments, not properly carried over into the bed file (covered with a bed entry although they should be excluded for a coverage calculation).

    I had a similar issue with RNA-Seq splice-mapped reads and BEDTools, and could fix it by using the "-split" argument with the bamToBed converter (splice reads are then splitted into two bed entries) - but if it is due to other non-matching CIGAR operations you might need a closer look at the read alignments themselves at those differing positions.

    Comment


    • #3
      Thank you arvid,

      I tried bamToBed with -split, no changes to the result, since my bedfile only contains CCDS regions.

      coverageBed reports all the bases covered at the position, while samtools/depth may have some default CIGAR operation as filter, I need to look closer.

      Thanks again

      Comment

      Latest Articles

      Collapse

      • 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
      • seqadmin
        Techniques and Challenges in Conservation Genomics
        by seqadmin



        The field of conservation genomics centers on applying genomics technologies in support of conservation efforts and the preservation of biodiversity. This article features interviews with two researchers who showcase their innovative work and highlight the current state and future of conservation genomics.

        Avian Conservation
        Matthew DeSaix, a recent doctoral graduate from Kristen Ruegg’s lab at The University of Colorado, shared that most of his research...
        03-08-2024, 10:41 AM

      ad_right_rmr

      Collapse

      News

      Collapse

      Topics Statistics Last Post
      Started by seqadmin, Yesterday, 06:37 PM
      0 responses
      10 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, Yesterday, 06:07 PM
      0 responses
      9 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-22-2024, 10:03 AM
      0 responses
      49 views
      0 likes
      Last Post seqadmin  
      Started by seqadmin, 03-21-2024, 07:32 AM
      0 responses
      67 views
      0 likes
      Last Post seqadmin  
      Working...
      X