Running ShortStack

[Sow]

Hi,

I am trying to run ShortStack-3.3 with the following input..

$ perl ShortStack.pl [options] {--readfile {ats_1000.fa}} --genomefile sta.fa

But it returns me the following

Unknown arguments: [options] {--readfile {ats_1000.fa}}

ShortStack version 3.3
Usage: ShortStack [options] {--readfile <r> | {--bamfile <b> | --cramfile <c>}} --genomefile <g>

I'm still very new to perl. Could anyone tell me what seems to be the problem?

[GenoMax]

@sow:

Run the ommand as follows

$ perl ShortStack.pl --readfile ats_1000.fa --genomefile sta.fa

[options] is the spot where you include optional command modifiers

{} or <> generally indicate input/output placeholders where you provide real filenames (relative or full paths).

[mastal]

try

$ perl ShortStack.pl --readfile ats_1000.fa --genomefile sta.fa

[Sow]

Thank you very much!
Yes your code worked just fine. Learned some basic syntax in the process.

[Sow]

Hi,
I just ran ShortStack 3.3 on a very large genome but I only got about 20 miRNAs. Is shortstack always this conservative? i have played around a bit with all the different options but I still only see about 20 miRNAs at max. Has anyone encountered this problem before?