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  • SOAP2 alignment problem

    Hello there,

    I tried SOAP2 to do alignments on paired-end data from illumina but the output was obviously wrong. Can anybody tell me where the problem is? Thanks!

    Command:
    soap -D human_g1k_v37.fasta.index -a s4.1.fastq -b s4.2.fastq -o soap_test_soap.soapaln -2 soap_test_soap_unpaired.soapout -p 12

    Version:
    Program: SOAPaligner/soap2
    Compile Date: Sun Aug 22 11:51:04 CST 2010
    Author: BGI shenzhen
    Version: 2.21
    Contact: [email protected]

    System:
    Linux 2.6.18-164.el5 #1 SMP Thu Sep 3 03:28:30 EDT 2009 x86_64 x86_64 x86_64 GNU/Linux

    STDERR:
    Begin Program SOAPaligner/soap2
    Tue Apr 16 11:13:43 2013
    Reference: human_g1k_v37.fasta.index
    Query File a: s4.1.fastq
    Query File b: s4.2.fastq
    Output File: soap_test_soap.soapaln
    soap_test_soap_unpaired.soapout
    Load Index Table ...
    Load Index Table OK
    Begin Alignment ...
    131072 ok 26.06 sec
    262144 ok 27.69 sec
    ...
    76229342 ok 17.47 sec
    Total Pairs: 38114671 PE
    Paired: 491344 ( 1.29%) PE
    Singled: 56747655 (74.44%) SE
    Total Elapsed Time: 17743.43
    - Load Index Table: 27.63
    - Alignment: 17715.80

    SOAPaligner/soap2 End
    Tue Apr 16 16:09:27 2013

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