Genetic Simulation Resources

I just came across a useful repository of genetic simulation resources I thought would make a good addition to Genome Toolbox.  The site, aptly called Genetic Simulation Resources (GSR), provides a detailed listing of over 80 useful software applications available for genetic simulations.  The NCI sponsored catalog aids in scanning through available simulation programs, comparing similar applications, and quickly identifying the most appropriate software application for a particular study.  In addition to providing a description and external link, literature citations are also listed for many of the simulation packages.  If you are the developer of a genetic simulation resource that is not listed in the GSR repository, you can submit a request to add it.  Overall, a great resource for simulating data for genetic studies that may help you avoid reinventing the wheel by programming a de novo simulation routine.  A good first place to check.

Change Citation Reference Style in EndNote X6

I was quite happy with Mendeley as my reference manager for a while, but recently it has been difficult to produce certain reference styles for lesser known journals.  Added to the difficulty of collaborating with others on manuscripts, I ultimately chose to convert to EndNote (non-open source, paid software...boo).  In all honesty, its not too bad and has plugins for Microsoft Word that work a lot like Mendeley.  When setting things up, I found importing journal citation styles could be a bit tricky, especially for newbies, so here is a quick primer to help out.

First go to Edit>Output Styles and look to see if the style you want is listed in the drop down menu.  If you see it you are in luck.  If not, click on Open Style Manager....

The EndNote Styles dialogue box will pop up.  There should be a list of styles that come pre-loaded with your installation.  If you see the journal style you need in the list, simply click the box next to the style so it is checked, exit out of the dialogue box, and click on that same style in the Edit>Output Styles menu.  If you don't see the reference style you need, keep reading.

To find additional styles, click on the Get More on the Web... button in the EndNote Styles dialogue box.  This will open the EndNote Output Styles Download site in your default web browser.  Use the fields to search for your style and if you find it click to download it.  Once downloaded, double click or drag your style into the EndNote.  A dialogue box with that style should pop up.  If everything looks fine, click File>Save As, delete copy from the style's name and save it.  To use it, check the box next to the style name and select it from the Edit>Output Styles menu.

If you don't find the style you need on the EndNote site, you can create your own style under Edit>Output Sytles>New Style....  A dialogue box named Untitled Style will pop up and you can begin to create a new style that matches your needs.  You are on your own here.  I have little experience with this.  Some tips are to start with a style that is close to what you need and edit it (ie: go to Edit>Output Styles>Edit "StyleNameHere", where StyleNameHere is the name of the style close to what you want).  Just be sure to save your style before closing out of the dialogue box.

Hope this helps.  Feel free to leave tips, helpful suggestions, or comments on anything I left out.

Download Complete Genomics Reference Files

A reference genome is needed when using cgatools on Complete Genomics data.  Here are links to the ftp sites that contain the reference compact randomly accessible reference (.crr) files.  Just use the wget command from a UNIX cluster to download.

NCBI Build 36:
ftp://ftp.completegenomics.com/ReferenceFiles/build36.crr

NCBI Build 37:
ftp://ftp.completegenomics.com/ReferenceFiles/build37.crr

The next step is to verify that the file downloaded completely.  Run one of the following commands at the command prompt depending on the version of the .crr file you downloaded.


The file output should look like this for build 36.


And this for build 37.

Create Reference FASTA File

A lot of sequencing programs and analyses require a reference genome FASTA file to run.  Since I didn't have a reference genome in my possession, I looked into making one of my own.  Here is the code I used to create an indexed reference sequence file from the UCSC ftp site that would be compatible with GATK.  When concatenating the chromosomes together, make sure they are in the same order and the same length as the .bam file you want to use it with.



After running GATK for the first time, a hg.19.dict file is also created.