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

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

illumina splicing
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updated by Shawn Baker • Shawn Baker • written by Doctoroots Doctoroots

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

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written by User 59 User 59

it comes with the illumina alignment tools package

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written by Doctoroots Doctoroots

2 answers

From what I can tell you are using an old script and an old version of CASAVA. If you contact Illumina tech support directly (Techsupport-ilmn@illumina.com) they can give you all the details you need.

Shawn Baker (Illumina)

• 2 views • link
written by Shawn Baker • Shawn Baker

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.

• 2 views • link
updated by Ram Ram • written by Paulo Nuin Paulo Nuin

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