How To Generate Splice Junction Set Using Illumina'S Splice_Sites.Pl Script?

Question

[Doctoroots]

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?

thanks

[User 59]

Could you provide a pointer as to where you have obtained this script?

[Doctoroots]

it comes with the illumina alignment tools package

[Doctoroots]

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

Answer 1

[Shawn Baker]

From what I can tell you are using an old script and an old version of CASAVA. If you contact Illumina tech support directly ([e-mail]) they can give you all the details you need.

Shawn Baker (Illumina)

Answer 2

[Paulo Nuin]

As I'm not familiar with this script, my best bet would be to run perl in debug mode with the command

perl -d <script name> <input>

With this you would be able to see if there's anything blocking the process run or you need to enter anything else. You might also be able to see how the script is operating and maybe find which part of the code might be giving you trouble.