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  • Picard SamToFastq strange behavious

    Dear all,

    I am using picard SamtoFastq in oredr to convert BAM/SAM to fastq. I have a paired end sample. I am using following command:-

    java -jar SamToFastq.jar INPUT=input.bam FASTQ=input_1.fastq SECOND_END_FASTQ=input_2.fastq VALIDATION_STRINGENCY=LENIENT

    The command runs without error and generate two file. Now the problem is input_1.fastq has all the reads where as input_2.fastq is empty(o byte file). I have no idea why it's happening. I tried following option but no luck,
    1) Sorted bam -> SamToFastq
    2) BAM to SAM -> SamToFastq

    Any suggestion would be very helpful.

    Thanks,
    Reema SIngh

  • #2
    Maybe you BAM file is not a paired end sample. Check it manually.

    Comment


    • #3
      Originally posted by TiborNagy View Post
      Maybe you BAM file is not a paired end sample. Check it manually.
      Thanks TiborNagy,

      You are right,my file is not paired..

      Comment

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