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  • Adding read group and Platform information

    Hi

    I am using BWA for alignment of my *.fastq files to get *.sam as an output. I have observed that *.sam lacks the RG and PL header.

    My Fastq looks like this
    @R0174436_0092:1:2:853:5576#0/1
    NACAACTTGAAGCAAAGGCAGGAAGCCTTGAAGCCGANNCAGAGAGGGGG
    +R0174436_0092:1:2:853:5576#0/1
    BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB

    and sam looks like this
    (partial header)
    @SQ SN:chr1 LN:247249719
    @SQ SN:chr2 LN:242951149
    @SQ SN:chr3 LN:199501827

    R0174436_0092:1:2:853:5576#0 16 chr4 79804636 25 50M * 0 0 CCCCCTCTCTGNNTCGGCTTCAAGGCTTCCTGCCT
    TTGCTTCAAGTTGTN BBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBB XT:A:U NM:i:3 X0:i:1 X1:i:0 XM:i:3 XO:i:0 XG:i:0 MD:Z:1
    1C0T36C0

    the BWA script i used

    bwa aln -l 32 -t 4 genome sequence1 > aln_1.sai
    bwa aln -l 32 -t 4 genome sequence2 > aln_2.sai
    bwa sampe genome aln_1.sai aln_2.sai sequence1 sequence2 > out.sam

    Do i need to add another index file or do i have some parameter to introduce to add RG and PL header to my sam file.

    Thanks

    Saurabh

  • #2
    Please see http://seqanswers.com/forums/showthr...5327#post25327 for multiple solutions

    Comment


    • #3
      Thanks Brugger !!, i will definitely try this..

      Comment

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