James Lindsay's Portfolio

HTS Analysis with SGI

admin — Thu, 12 Aug 2010 19:28:41 +0000

Uncrating and bringing into the building.

Stay tuned for a series of updates describing my experience with using an SGI Altix UV 100 with 512GB RAM, 48 Cores to process and analyze sequencing data generated on 454, SoliD and Illumina platforms. Check out this picture of our lab manager and myself taking the computer for a joy ride around campus… Or rather removing it from its packaging to fit it through the buildings doors. In subsequent posts I will describe the whole process of choosing, obtaining and using this machine to support data analysis and bioinformatics algorithm development.

RepeatMasker on the cluster

admin — Mon, 12 Jul 2010 18:09:04 +0000

Many organisms genomes contain a high percentage of so called “repetitive elements”, and the study of these elements is a very active area of research. After a research group has created a draft assembly of some organisms genome, usually the next step is to start annotating various genomic features such as genes and repetitive elements. One tool, RepeatMasker, by the Institute for System Biology has emerged as a defacto standard in de novo, and database repeat identification and classification.

I’ve added some more code to the NextGenScripts page, one little script helps split fasta formatted files into smaller pieces. The other is a script to run RepeatMasker on a cluster, this speeds up the programs execution time greatly. None of my code mentions how to install or work with RepeatMasker, so please follow the above link to install the software first.

Preferred Tools and NextGenScripts

admin — Thu, 01 Jul 2010 00:15:19 +0000

I added a new page titled Preferred Tools which is nothing more than a list of tasks and the tools I use to accomplish them. I hope it is useful to people out there. Secondly I started adding some code to my repositories. You can check out both pages by clicking links in the right hand menu.

Download Whole Genomes Quickly from NCBI

admin — Wed, 30 Jun 2010 22:04:10 +0000

Here is a quick command line script that should work on any linux system with wget. This command will download chromosomes 1- 8 for the possum. You would need to modify the list of numbers to be “X Y M Un” to get the non-numeric chromosomes.

for i in 01 02 03 04 05 06 07 08; do wget "ftp://ftp.ncbi.nih.gov/genomes/Monodelphis_domestica/CHR_${i}/mdm_ref_chr${i}.fa.gz"; done;

You can do this for any species or really any organized FTP site. Here is the link to the NCBI genome ftp site.

Welcome

admin — Tue, 29 Jun 2010 02:25:08 +0000

Welcome to my updated portfolio. Please stay tuned as I add information about my current work, publications and even some code.