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  • 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

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