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
      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, 07-10-2024, 07:30 AM
    0 responses
    23 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 09:45 AM
    0 responses
    198 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-03-2024, 08:54 AM
    0 responses
    209 views
    0 likes
    Last Post seqadmin  
    Started by seqadmin, 07-02-2024, 03:00 PM
    0 responses
    191 views
    0 likes
    Last Post seqadmin  
    Working...
    X