i have been using the command line :
perl Splicesites.pl --refSequences=/path/to/mousefasta/ /path/to/mousemm9refFlat.txt mouse_splice
and it seems the terminal is idling, as if it is waiting for another param.
i also tried : perl Splicesites.pl --refSequences=/path/to/mousefasta/ < /path/to/mousemm9refFlat.txt > mouse_splice
and it seemed to work - it finished gathering and consolidating splice sites coordinates but when extracting sequences, it skipped all the chromosomes.
is there something im missing?
Could you provide a pointer as to where you have obtained this script?
it comes with the illumina alignment tools package
it comes with the illumina alignment tools package, usage information is provided in the guide : http://watson.nci.nih.gov/solexa/CASAVA1.6_User_Guide_15009919_A.pdf i thought i was following the instructions right, but apparently im doing something wrong