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  • m_elena_bioinfo
    Member
    • Oct 2009
    • 99
    #1

    solid2fastq paired-end

    Hi SOLiD user,
    i have to align SOLiD reads to human genome. They are from a paired-end experiment, so I have a csfasta and a quality file for F3 and for F5-P2.

    For example I have these files:
    solid_data_F3.csfasta
    solid_data_F5-P2.csfasta
    solid_data_F3_QV.qual
    solid_data_F5-P2_QV.qual

    To obtain a fastq file, is correct the following command?
    > solid2fastq.pl solid_data_ output

    In this way, i obtain only one file to align to genome. Is it correct?
    thanx to everybody
    ME
    Tags: None
  • nilshomer
    Nils Homer
    • Nov 2008
    • 1283
    #2
    Originally posted by m_elena_bioinfo View Post
    Hi SOLiD user,
    i have to align SOLiD reads to human genome. They are from a paired-end experiment, so I have a csfasta and a quality file for F3 and for F5-P2.

    For example I have these files:
    solid_data_F3.csfasta
    solid_data_F5-P2.csfasta
    solid_data_F3_QV.qual
    solid_data_F5-P2_QV.qual

    To obtain a fastq file, is correct the following command?
    > solid2fastq.pl solid_data_ output

    In this way, i obtain only one file to align to genome. Is it correct?
    thanx to everybody
    ME
    What package is the "solid2fastq.pl" script from?

    Comment

    • m_elena_bioinfo
      Member
      • Oct 2009
      • 99
      #3
      i'm using solid2fastq.pl in bwa0.5.7 package

      Comment

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