Sunday, July 26, 2009

Researchers get hands-on practice using GeneSifter to analyze Next Gen data and SNPs at the UT-ORNL-KBRIN 2009 summit

As the recently-published meeting report attests (1), while the much of the genomics world was bemoaning the challenge of working with Next Generation DNA sequence (NGS) data, attendees at the UT-ORNL-KBRIN summit got an opportunity to play with the data first-hand. These lucky researchers, among the first in the nation to work with NGS data outside of a genome center, were participants in a hands-on education workshop presented by Dr. Sandra Porter from Digital World Biology.

This opportunity came about through a collaboration between Geospiza and Digital World Biology. Data were loaded and processed through GeneSifter’s analysis pipelines before the workshop to align data to reference sequences and perform the secondary analyses. During the workshop, Porter led researchers through typical steps in the tertiary analysis phase. Workshop participants were able to view gene lists and analyze information from both Illumina and SOLiD datasets. The analyses included: working with thumbnail graphics to see where reads map to transcripts and assess coverage, viewing the number of reads mapping to each transcript, and comparing the number of reads mapping to different genes under different conditions to investigate gene expression.

An additional workshop focused on using iFinch and FinchTV to view SNP data in chromatogram files generated by Sanger sequencing and working with structures to see how a single nucleotide change can impact the structure of a protein.

1. Eric Rouchka and Julia Krushkal. 2009. Proceedings of the Eighth Annual UT-ORNL-KBRIN Bioinformatics Summit 2009. BMC Bioinformatics 10(Suppl 7):I1doi:10.1186/1471-2105-10-S7-I1.

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