oligoMatch from ucsc

Question

[theodore]

Hallo people, one quick question, how does oligoMatch from ucsc (kent lab tools) works? I am asking because for some reason it does not work for me. I am downloading the oligomatch from ucsc exe folder (the 64bit version), I download the hg19 genome in fasta (i have also tried the 2bit) hg19.fa (or hg19.2bit) I create an other fasta file that corresponts to the sequence I want to search for: apoi.fa

>apoi
RAATTY

and then i run the following command:

./oligoMatch apoi.fa chr19.fa

the outcome is the default message as if I had no files.

oligoMatch - find perfect matches in sequence.
usage:
   oligoMatch oligos sequence output.bed
where "oligos" and "sequence" can be .fa, .nib, or .2bit files.
The oligos may contain IUPAC codes.

Any idae what I am missing?

Thank you all

[Pierre Lindenbaum]

Hello theodore!

It appears that your post has been cross-posted to another site: https://groups.google.com/a/soe.ucsc.edu/forum/#!topic/genome/CMdFjv18Kvc

This is typically not recommended as it runs the risk of annoying people in both communities.

Answer 1

[GenoMax]

Missing a name (e.g. ./oligoMatch apoi.fa chr19.fa output.bed) to hold the output.

[theodore]

that's the worst omission, ever made! thank you and sorry for my stupidity!