OMICtools is a workflow for genomic, transcriptomic, proteomic, and metabolomic data analysis. All tools have been classified by omic technologies (NGS, microarray, PCR, MS, NMR), applications and analytical steps. Publication: OMICtools: an informative directory for multi-omic data analysis

RefFinder
  (4/5)
As it uses all the 4 software to determine the best reference gene, i would like to know which one among them is the most reliable?
Posted by Newbie on Jul 04, 2015
GenPlay
  (5/5)
Great software

Similar to IGV but much faster and a lot more functions
Posted by Eric on Jun 30, 2015
Path encoding
  (2/5)
This tool is indeed very efficient in compressing fastq files.
Unfortunately in the compressed file you lose all info in the sequence identifier and the quality score.
Posted by Mmoisse on Jun 25, 2015
LW-FQZip
  (1/5)
I tried this tool but the compression doesn't seem to be that great.

I could compress the example fastq of 31M was to 8.6M. This is exactly the same size as if you would use gzip on this file. Using bzip2 the file size is reduced even further to 7.3M.

Additionally when I tried to compress my own fastq files (human) I got he error 'error genome file size'. After solving this issue in a hard coded way, I got a buffer overflow using the LWFQZip -c command.
Posted by Mmoisse on Jun 25, 2015
Genes2GO
  (5/5)
Very useful tool!
Posted by Sushil on Jun 22, 2015
RefFinder
Site down again :( :(
Posted by Newbie on Jul 04, 2015
GlycoWorkbench
Hello,

I have a problem when I try to open some files with previously saved workspace (annotated peak list with structures from database, .gwp), and annotation files (.gwr). Some files may be opened without errors, but no regularity has been detected.
It’s beautiful software and it’s a pity to lose data.
My contacts: krasnov@biocad.ru

Soft ver. GlycoWorkbench 2.1 stable (build:146)
Java 7 Update 79
System: Windows XP Professional (5.1, 2600)
Processor: Intel Core2 Quad CPU Q6700 @ 2.66GHz (4CPUs)
Error code:

java.lang.ArrayIndexOutOfBoundsException: -1
at java.util.Vector.elementData(Unknown Source)
at java.util.Vector.elementAt(Unknown Source)
at org.eurocarbdb.application.glycoworkbench.PeakAnnotationCollection.elementAt(PeakAnnotationCollection.java:168)
at org.eurocarbdb.application.glycoworkbench.PeakAnnotationCollection.getPeakAnnotation(PeakAnnotationCollection.java:393)
at org.eurocarbdb.application.glycoworkbench.plugin.reporting.AnnotationReportDocument$SAXHandler.finalizeContent(AnnotationReportDocument.java:1036)
at org.eurocarbdb.application.glycanbuilder.SAXUtils$ObjectTreeHandler.endElement(SAXUtils.java:307)
at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanEndElement(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown Source)
at org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(Unknown Source)
at org.eurocarbdb.application.glycanbuilder.SAXUtils.read(SAXUtils.java:385)
at org.eurocarbdb.application.glycoworkbench.GlycanWorkspace.read(GlycanWorkspace.java:635)
at org.eurocarbdb.application.glycanbuilder.BaseDocument.open(BaseDocument.java:330)
at org.eurocarbdb.application.glycanbuilder.BaseDocument.open(BaseDocument.java:312)
at org.eurocarbdb.application.glycoworkbench.GlycoWorkbench.onOpen(GlycoWorkbench.java:3078)
at org.eurocarbdb.application.glycoworkbench.GlycoWorkbench.onOpen(GlycoWorkbench.java:2965)
at org.eurocarbdb.application.glycoworkbench.GlycoWorkbench.actionPerformed(GlycoWorkbench.java:3631)
at org.pushingpixels.flamingo.api.common.AbstractCommandButton.fireActionPerformed(AbstractCommandButton.java:614)
at org.pushingpixels.flamingo.api.common.AbstractCommandButton$ActionHandler.actionPerformed(AbstractCommandButton.java:566)
at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)
at org.pushingpixels.flamingo.api.common.model.ActionRepeatableButtonModel.setPressed(ActionRepeatableButtonModel.java:123)
at org.pushingpixels.flamingo.internal.ui.common.BasicCommandButtonListener.mouseReleased(BasicCommandButtonListener.java:147)
at java.awt.AWTEventMulticaster.mouseReleased(Unknown Source)
at java.awt.Component.processMouseEvent(Unknown Source)
at javax.swing.JComponent.processMouseEvent(Unknown Source)
at java.awt.Component.processEvent(Unknown Source)
at java.awt.Container.processEvent(Unknown Source)
at java.awt.Component.dispatchEventImpl(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)
at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)
at java.awt.Container.dispatchEventImpl(Unknown Source)
at java.awt.Component.dispatchEvent(Unknown Source)
at java.awt.EventQueue.dispatchEventImpl(Unknown Source)
at java.awt.EventQueue.access$300(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.awt.EventQueue$3.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.awt.EventQueue$4.run(Unknown Source)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)
at java.awt.EventQueue.dispatchEvent(Unknown Source)
at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.pumpEvents(Unknown Source)
at java.awt.EventDispatchThread.run(Unknown Source)
Posted by Krasnov Ilya on Jul 01, 2015
comrad
Hi,

I WANT to run one of your software Comrad for the fusion detection.

In the config file (config.txt), i am setting the files path.

I could not found the following files.


# These files are provided in the downloadable dataset from the following url:
# http://compbio.bccrc.ca/wp-content/uploads/2010/04/comrad_data.tar.gz
ab_parts_filename = (dataset_dir)/abParts.txt
ab_parts_regions = (dataset_dir)/abParts.regions
repeat_regions = (dataset_dir)/repeats.txt
region_filter = (dataset_dir)/region_filter.txt


These files are not present at the given link. From where I can download these file now ???

PLease help me.
Posted by shailesh kumar on Jun 30, 2015
FPPI
The web page for the database doesnt open. Shows error..
Posted by gayatri on Jun 30, 2015
Poly Peak Parser
It is not possible to open the website
Posted by Jorge Carretero-Ortega on Jun 26, 2015