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.

To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the link below how to install this certificate.

http://www.myexperiment.org/files/148

The myExperiment pack http://www.myexperiment.org/packs/45 contains the workflow, the input and a test input. The whole input set is large. It takes about 6 hours on a 3 GHz Linux pc with 24 Gig RAM. The test input set can be run on almost any computer with Taverna and R installed. This set takes approximately 10 minutes.

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