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Old 01-26-2012, 12:23 PM   #1
jlelias
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Default Novoalign Output Missing

Hi,
I have run novoalign in multiple ways, but each time when the program finishes running, I cannot find the output file! -o just specifies the output format. There are no errors during the run. Can you tell me where the alignment file is or how I could find it?
Thank you!
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Old 01-26-2012, 03:17 PM   #2
Heisman
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./novoalign -o SAM -d [file.novoindex] -f [read_1] [read_3] 1> [output.sam] 2> [output.metrics]

That should be a basic way to run it.
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Old 01-27-2012, 08:49 AM   #3
jlelias
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That worked perfectly. THANK YOU!!
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Old 11-06-2012, 11:26 PM   #4
TabeaK
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Hi guys!

Just resurrecting this thread - had exactly the same problem as the OP, but now it works.

Just what exactly are the output.metrics?
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Old 11-07-2012, 01:55 PM   #5
Jiafen
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Like the number of reads, number of aligned etc.

Quote:
Originally Posted by TabeaK View Post
Hi guys!

Just resurrecting this thread - had exactly the same problem as the OP, but now it works.

Just what exactly are the output.metrics?
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