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  • conver bam to fastq

    hi, I try to convert the bam produced by pacbio sequel platform to fastq file. The output file showed the detailed sequence, but the quality values were all "!". both "bamToFastq" and "samtools bam2fq" were used.

    @m54061_161228_010008/4194368/0_66
    AGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
    +
    !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

  • #2
    bam to fastq conversion is actually not something particularly difficult...
    Could you paste the corresponding sam record to your example
    What about the original data (before alignment); how does this look?

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    • #3
      Sequel data does not have a per base QV value for raw reads. If you calculate CCS first then the quality values will be meaningfully populated.

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      • #4
        May this will help? https://github.com/PacificBiosciences/bam2fastx

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