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  • Trouble with SRA toolkit sam-dump

    I catch a SRA file from NCBI
    and i can convert that file to .fastq by using fastq-dump

    but when i use sam-dump an error happened

    " sam-dump.2.3.2 err: name not found while resolving tree within virtual file system module - cannot open tab 'ex.sra'


    (ex.sra is my file)

    thanks for ur help!

  • #2
    Have a look at this thread (not sure if it will help in this specific instance) : http://seqanswers.com/forums/showthread.php?t=28741 Is the SRA file you are working with using reference based compression?

    You should also contact SRA tech support with additional specifics about the error (which exact SRA # etc). There are instances where SRA files have errors in them.

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