Mapping OligoNucleotides to an assembly

Created: 2009-02-13 09:05:35      Last updated: 2009-02-13 09:08:20

This workflow maps the input oligo set to an assembly.

It first performs an alignment using the BioMoby Blat and Blast service provided by WUR (www.bioinformatics.nl). Next, for each hit, tries to find the corresponding transcripts and genes using a biomart webservice. The final task is an analysis task using RShell. It calculates for each oligo to which class it belongs:

1 single hit
2-4 multiple hits single transcript*
5-7 mulitple hits multiple transcripts*
8 single hit, discarded**
9 multiple hits single transcript, discarded**
10 multiple transcripts, discarded**
11 multi gene, discarded
12 no transcript***
13 no transcript, discarded*
* classified on the criteria intron spanning only, possible intron spanning and no intron spanning.
** hit(s) do not meet high stringency threshold
*** no transcript found but hit(s) meet high stringency threshold.

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