The pipeline runs as follows:

1) digest virtual transcrptome, extract tags, look for internal polyA

./tagger.pl virtual_transcriptome > possible_polyA

2) evaluate empirical tags to look for thise which me be the result of
   NlaII partial digestion  

./partial.pl meta_lib.txt > NlaIII_partial

3) run the alternative splicing analysis

./altsplice.pl metta_lib.txt