Whether you are a novice or an expert in NGS sequencing technologies, GTAC can help you design a study, prepare DNA or RNA libraries, sequence samples, and analyze the data.
Our pipeline fully supports the goal of exome or targeted sequencing to identify SNPs within the target sequence. We use proven tools, such as Novoalign for fast, accurate read alignments and SAMtools for SNP detection. Additionally, the pipeline identifies potential indels, but not nearly as accurately as it does SNPs. Identified SNPs are annotated using SeattleSeq (human) or snpEff (mouse). Data is returned as a flat file or spreadsheet of annotated variants with respect to the reference genome sequence. Additional downstream analyses or filtering of SNPs against other samples may be available for a nominal rate.Reads are aligned to the genome using Novoalign. PCR duplicates are removed and coverage statistics are reported. SNPs are identified using SAMtools and annotated using snpEFF, a tool that predicts the effects of variants on genes.
Here is an example of expression analysis output: https://htcf.wustl.edu/files/3kMJmRXA/
For more information see:
Sequencing reads are aligned with Novoalign. Peaks are detected using MACs. If sample/control information is provided by the investigator, we can include that in the analysis.