SEQanswers

SEQanswers (http://seqanswers.com/forums/index.php)
-   Bioinformatics (http://seqanswers.com/forums/forumdisplay.php?f=18)
-   -   Novoalign Output Missing (http://seqanswers.com/forums/showthread.php?t=17136)

jlelias 01-26-2012 12:23 PM

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!

Heisman 01-26-2012 03:17 PM

./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.

jlelias 01-27-2012 08:49 AM

That worked perfectly. THANK YOU!!

TabeaK 11-06-2012 11:26 PM

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?

Jiafen 11-07-2012 01:55 PM

Like the number of reads, number of aligned etc.

Quote:

Originally Posted by TabeaK (Post 88675)
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?



All times are GMT -8. The time now is 01:45 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.