Pack: Package: mapping oligonucleotides to an assembly

Created: 2008-12-11 12:02:47 Last updated: 2009-01-22 09:06:26

Live view

Title: Package: mapping oligonucleotides to an assembly

Description

This package contains all elements required to run the RShell use case "Mapping oligonucleotides to an assembly"

Items (5)

File: Input for Mapping oligonucleotides to an assembly (Wassinki)

Added by Wassinki ... more than 1 year ago (2008-12-11 12:13:38)

File: Installing java certificates for services using SSL (Wassinki)

Added by Wassinki ... more than 1 year ago (2008-12-11 12:13:54)

Description:

This jar file, designed by sun microsystems, helps you to install certificates for java to access services using a secure socket.

The complete documentation of this small java tool, including its source, can be found at: http://blogs.sun.com/andreas/entry/no_more_unable_to_find

In this document, I will explain how to create a keystore holding the certificate required to access services provided by www.bioinformatics.nl .

To install the certificate for www.bioinformatics.nl, do the following steps:

download the jar file
execute the jar: "java -jar InstallCert.jar www.bioinformatics.nl"
The program asks you to choose which certificate to use, choose 1
A certificate file named "jssecacerts" is created. Put this file in the "lib/security" of your java installation. In case you have multiple java installations, you can decide to place it in all installations. Otherwise, you have to determine which installation taverna uses.
(In Windows, you can do this with "set JAVA_HOME", in linux, "echo $JAVA_HOME")
Before you can start services provided by www.bioinformatics, you possibly have to restart Taverna.
Good luck

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.
Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.
Neither the name of Sun Microsystems nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

Workflow: Mapping OligoNucleotides to an assembly (Wassinki)

Added by Wassinki ... more than 1 year ago (2008-12-11 12:13:13)

Description:

Version info

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.

Workflow description

We used RShell in the design process of a Zebrafish microarray
(supp. info Figure S1 and Figure S2). A microarray with 15k probes
of 60-mer oligonucleotides was designed on gene sequences from
Vega (http://vega.sanger.ac.uk/Danio_rerio) and Ensembl
(http://www.ensembl.org/Danio_rerio/) that are also known
in the Zebrafish Information Network (http://zfin.org) (for zebra
fish, the VEGA set is not a subset of the Ensembl set) of the genome
DNA-sequence assemblies and to judge the agreement that exists between
the different assembly annotations, we mapped the Vega-designed probes
onto the Ensembl 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:

0 no hit
1 single hit, single transcript, single gene
2 multiple hits, single transcript, single gene, intron spanning
3 multiple hits, single transcript, single gene, possible intron spanning *
4 multiple hits, single transcript, single gene, no intron spanning
5 multiple hits, multiple transcripts, single gene, intron spanning
6 multiple hits, multiple transcripts, single gene, possible intron spanning *
7 multiple hits, multiple transcripts, single gene, no intron spanning
8 single hit, does not meet additional criteria **
9 multiple hits, single transcript, do not meet additional criteria **
10 multiple hits, multiple transcripts, do not meet additional criteria **
11 multiple hits, multiple genes
12 no transcript found but hit(s) meet additional criteria **
13 no transcript found and hit(s) do not meet additional criteria **
14 multiple hits, single transcript, single gene plus hit without transcript found and hits
meet additional criteria **
* Oligo below e-value cut-off 1e-12, but also intron spanning criteria met.
** Additional criteria: either e-value below 1e-12 or intron spanning.

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.

File: Results of the Mapping oligonucleotides to an assembly (Wassinki)

Added by Wassinki ... more than 1 year ago (2008-12-19 09:54:37)