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  • Using samtools to analyze bwa output

    I have a query file with 70,000 lines of sequences and when I do the
    Code:
    bwasw
    each sam output file is about 35 mb and obviously contains all the sequence lines. I need to perform the alignment on about 1000 files, so you can imagine that I don't want to have 35 gigs worth of output to sort.

    I am trying to get rid of the non-aligned reads from the SAM output file ans I searched through forums and tried the following code with no avail.

    Code:
    ./samtools view -bS -f 4 testing.sam > output.bam
    All my sam files give the following error:

    Code:
    [samopen] SAM header is present: 1 sequences.
    [sam_read1] reference '0' is recognized as '*'.
    Parse warning at line 3: mapped sequence without CIGAR
    Parse error at line 3: missing colon in auxiliary data
    Aborted (core dumped)

    Here's what a part of my sam files looks like


    Code:
    @SQ	SN:gi|89106884|ref|AC_000091.1|	LN:4646332
    
    	4	*	0	0	*	*	0	0	<CGTAAAAAGGA> 	*
    	4	*	0	0	*	*	0	0	<TAGCCGTAGGG>   *
    I'd appreciate help with this!

  • #2
    There's no read name in the SAM records you list.

    Comment


    • #3
      But this is the output I get from bwa. how should i fix this?

      Comment


      • #4
        Post the BWA help mailing list. It looks like a bug to me. Make sure you include a test case.

        Comment


        • #5
          Before I do that, I want to make sure I am not wrong. Here is the code I used for the bwa:

          Code:
          ./bwa bwasw INDEXES/AC_000091.fna QUERY/635plus104_500bp_reads.fasta > results.sam
          The input AC_000091.fna was the indexes created with the following command:

          Code:
          ./bwa index AC_000091.fna "AC_000091.fna";
          and the query file was a FASTA sequence file.

          So, in theory this should have worked?

          Comment

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