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  • Input to BWA from multiple Lanes

    hi,

    I have paired end data from multiple lanes (illumina pipleine) in qseq format.
    i convert all the qseq files to fastq lane wise.
    Combine the first sequences in one file and the next sequences in the other file of a particular lane.
    Then follow the BWA pipeline i.e.
    index the reference, find the suffix array coordinates ('aln') and then use the 'sampe' command to get the sam files.

    But since i have data from multiple lanes, so should i just combine the sam files ?
    or Follow a different workflow for creation of input files(fastq) for BWA ?

    Please provide some suggestions

    Thanks.

  • #2
    I assume the data from different lines belongs to the same sample. If so, yes, you can merge the BAM files per each line (picard tools) and align with BWA.
    -drd

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    • #3
      You can use Unix cat to combine files. At the command line, enter "cat file 1.fq file2.fq > combined_file.fq

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