Novoalign Output Missing

[jlelias]

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]

./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]

That worked perfectly. THANK YOU!!

[TabeaK]

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]

Like the number of reads, number of aligned etc.

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?