Analysis Pipelines

We are continously adding new capabilities and expand our expertise.

• See the Request Analysis page for more information on getting your data analyzed.
• New users should consult the Analysis Examples for examples of what each report includes.

Note

For optimal results we may need hand tune the various parameters to be most appropriate for your project. You will need to Contact us to discuss the details.

Metagenomics Pipeline

We primarily use the mothur package to automate inital data analysis. The default report will include:

• Generate statistics on the quality of reads for each barcoded sample
• Bayesian sequence classification based on the current taxonomy
• Community richness estimators
• Community structure calculators
• Community similarity measures

ChIP-seq Pipeline

Currently, the ChIP-seq data analysis uses the solid pipeline to perform genome alignments in high performance servers (lionxi, hammer) using the SHRiMP mapping utility. The data from the log files in the alignment runs are compiled to generate the analysis report. The initial (default) report would include:

• Project information
• Sample preparation report
• Sequencing information
• Alignment statistics
• Peak calling statistics

Note

Due to the differing nature of each alignment run, the requests should be made by filling out the data information sheet.