Mapping OligoNucleotides to an assembly

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In chronological order:

1. Mapping oligonucleotides to an assembly

   Created by Wassinki on Thursday 11 December 2008 12:11:59 (UTC)

   Last edited by Wassinki on Thursday 11 December 2008 12:25:55 (UTC)

2. Mapping OligoNucleotides to an assembly

   Created by Wassinki on Thursday 11 December 2008 12:26:50 (UTC)

   Last edited by Wassinki on Thursday 11 December 2008 12:32:04 (UTC)

3. Mapping OligoNucleotides to an assembly

   Created by Wassinki on Friday 19 December 2008 09:41:13 (UTC)

   Revision comment:

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   The newest version only takes into account the probes that have blast hits that map on exons. The BioMart sub workflow has been modified to do this by adding an extra BioMart processor and a beanshell processor to filter those blast hits that map on exons.

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   This workflow maps the input oligo set to an assembly.<o:p></o:p>

   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:<o:p></o:p>

   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.<o:p></o:p>

   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<o:p></o:p>

   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.<o:p></o:p>

   <o:p> </o:p>

   <o:p> </o:p>

4. Mapping OligoNucleotides to an assembly

   Created by Wassinki on Tuesday 03 February 2009 15:27:18 (UTC)

   Last edited by Wassinki on Tuesday 03 February 2009 15:33:01 (UTC)

   Revision comment:

   The former version of the workflow expected that results from BioMART only report transcripts when the query (the probe in our case) are entirely encapsulated in an exon of that transcript. However, the BioMart service also returns transcripts when the query is not or only partially overlapping with an exon in the stretch on the assembly on which a transcript is defined. This resulted in too many oligos classified as having multiple transcripts or having multiple genes.
    

5. Mapping OligoNucleotides to an assembly

   Created by Wassinki on Wednesday 04 February 2009 08:25:36 (UTC)

   Last edited by Wassinki on Wednesday 04 February 2009 08:26:04 (UTC)

6. Analysing workflows

   Created by Wassinki on Friday 13 February 2009 09:03:37 (UTC)

7. Mapping OligoNucleotides to an assembly

   Created by Wassinki on Friday 13 February 2009 09:05:35 (UTC)

   Last edited by Wassinki on Friday 13 February 2009 09:08:23 (UTC)