Trouble with SRA toolkit sam-dump

Chulab4121

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Join Date: May 2013

Posts: 2
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#1

Trouble with SRA toolkit sam-dump

05-17-2013, 10:29 PM

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!
Tags: sam-dump
GenoMax

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Join Date: Feb 2008

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#2

05-20-2013, 03:47 AM

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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Trouble with SRA toolkit sam-dump

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