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  • SAM to BAM problem

    Parse warning at line 27: mapped sequence without CIGAR
    Parse error at line 27: sequence and quality are inconsistent
    Aborted



    I used BWASW for alignment. Any help ??

    Comment


    • Originally posted by abi View Post
      Parse warning at line 27: mapped sequence without CIGAR
      Parse error at line 27: sequence and quality are inconsistent
      Aborted



      I used BWASW for alignment. Any help ??
      Was the file truncated at that line? Otherwise it'd be helpful to see that line of the SAM file.

      Comment


      • No the file was not truncated at line 27. Here is the line:

        0 chr4 96674301 60 227M * 0 0 TCTTTGAAACCAACGAGAACAAAGACACAACATACCAGAATCTCTGGGACACATTTAAAGCAGTGTGTAGAGGGAAATTTACAGCAGTAAATGCCCACAAGAGAATGCAGGAAAGATCTAAAATTGACACCCTAACATCAAAATTAAAAGAACTAGAGAAGCAAGAGCAATCACATTCAAAAGCTAGCAGAAGGCAAGAAATAACTAAGATCAGAGCAGAACTGAAG * NM:i:0 AS:i:227 XS:i:0


        I am using bwa-0.7.4 for my alignment .

        I must say that I used FASTA file for alignment and not FASTQ file. Here is a sample line from FASTA file:

        > MySpecies 207
        GGAGCCTTAAGGTTTGGTTATCGCCTTGTGTTTGTTTCTGGGGGTATCTGTGGGGTATGTGTTTCTGGCCATGTGTCTGTGTCTGTGTCTCTAGGCTGTCTTCTAGTCTCAGCTTGAGATCCACAGGCTTCAAGAGCTCAAGGGGGGAAAAGCCCAATTGTATATAAATTGTGAATGGGACTGATGCGTATGAGACAGGGAGGGTCT

        Comment


        • I have seen similar issues with BWA 0.7 greater, same command runs absolutely fine with 0.7 version of BWA.

          Comment


          • @abi , lh3, sbaheti, dpryan, Hena and rest

            I have the answer to you. There is a bug in newer versions of BWA. It does not produces right SAM files for those sequences which have their Fasta/Fastq files starting with > and a space. As an example:

            This will not produce right SAM files
            > My sequence

            This will produce right SAM files
            >My sequence


            Notice the difference in space after '>'

            Hope this helps. You can read more about me at www.tinyurl.com/abinarain

            Cheers
            Narain
            Last edited by narain; 06-05-2013, 09:40 AM.

            Comment


            • [samopen] SAM header is present: 84 sequences.
              [sam_read1] reference '121337031' is recognized as '*'.
              Parse warning at line 7932555: mapped sequence without CIGAR
              Parse error at line 7932555: sequence and quality are inconsistent
              Aborted (core dumped)


              I am getting this error... tried the suggestion on changing the MDI in the blast2sam.pl but it is still not working!

              Any suggestions will be appreciated.

              Comment


              • [samopen] SAM header is present: 84 sequences.
                [sam_read1] reference '121337031' is recognized as '*'.
                Parse warning at line 7932555: mapped sequence without CIGAR
                Parse error at line 7932555: sequence and quality are inconsistent
                Aborted (core dumped)

                The suggestion to change MDI in blast2sam pl did not work! Any suggestions will be appreciated.

                Comment


                • Blast2Sam won't work, because it is an outdated script (I have tried it several times without success). Try to align your sequences with bwa/bowtie.

                  Comment

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