Seqanswers Leaderboard Ad

Collapse

Announcement

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

  • BBMAP paired-end alignment problem

    Hi All

    I'm having a problem with aligning Illumina PE reads with BBMap version 35.92.

    Execution of

    Code:
    bbmap.sh overwrite=t ref=Z.fasta in=R1_001_val_1.100.fq in2=R2_001_val_2.100.fq minid=0.25 mappedonly=true out=out.sam  outu=unaligned_reads.fa maxindel=100000
    yields out.sam which contains only alignments of read1 even though the log info seems to suggest read2 reads were also aligned

    Code:
    Pairing data:           pct reads       num reads       pct bases          num bases
    
    mated pairs:            100.0000%             100       107.4763%              59558
    bad pairs:                0.0000%               0         0.0000%                  0
    insert size avg:          412.82
    
    
    Read 1 data:            pct reads       num reads       pct bases          num bases
    
    mapped:                 100.0000%             100       100.0000%              29779
    unambiguous:            100.0000%             100       100.0000%              29779
    ambiguous:                0.0000%               0         0.0000%                  0
    low-Q discards:           0.0000%               0         0.0000%                  0
    
    perfect best site:        0.0000%               0         0.0000%                  0
    semiperfect site:        35.0000%              35        35.1758%              10475
    rescued:                  0.0000%               0
    
    Match Rate:                   NA               NA        88.8176%              26449
    Error Rate:              65.0000%              65         4.4763%               1333
    Sub Rate:                65.0000%              65         0.3627%                108
    Del Rate:                 0.0000%               0         0.0000%                  0
    Ins Rate:                49.0000%              49         4.1136%               1225
    N Rate:                 100.0000%             100         6.7061%               1997
    
    
    Read 2 data:            pct reads       num reads       pct bases          num bases
    
    mapped:                 100.0000%             100       100.0000%              25636
    unambiguous:            100.0000%             100       100.0000%              25636
    ambiguous:                0.0000%               0         0.0000%                  0
    low-Q discards:           0.0000%               0         0.0000%                  0
    
    perfect best site:        0.0000%               0         0.0000%                  0
    semiperfect site:        26.0000%              26        25.3745%               6505
    rescued:                  2.0000%               2
    
    Match Rate:                   NA               NA        86.8232%              22258
    Error Rate:              74.0000%              74         4.9852%               1278
    Sub Rate:                74.0000%              74         0.8894%                228
    Del Rate:                 0.0000%               0         0.0000%                  0
    Ins Rate:                42.0000%              42         4.0958%               1050
    N Rate:                 100.0000%             100         8.1916%               2100
    As a test I then tried

    Code:
    bbmap.sh overwrite=t ref=Z.fasta in=R2_001_val_2.100.fq minid=0.25 mappedonly=true out=out.sam  outu=unaligned_reads.fa maxindel=100000
    Here read2 reads were aligned.

    Any ideas what is wrong with the first command line for the paired-end reads?

    Thanks

    Mark

  • #2
    Cross-posted and answered on Biostars:https://www.biostars.org/p/301541/

    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
    51 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