What: Binding site predictions and (new) basic localization analysis and gene identification for ChIP-chip experiments using NimbleGen tiling arrays. Originally designed for arrays with 350,000 - 400,000 oligos but may be used in other designs.These arrays should be relatively high density (i.e., < 100 bp spacing), as in ENCODE arrays. Contact Mark Bieda if you have questions. Do not use this for promoter arrays.
Who: Collaboration of the Farnham (website here) and Ludaescher labs. Analysis programs by Mark Bieda. Website by Tim McPhillips and Mark Bieda. Thanks to Mark Eschbach for website advice.
Methods: The statistical model and methodology used by the TAMALPAIS server is described in Bieda et al., 2006 Genome Research 16:595. Available here. The complete package of software (for Linux only) is available from Mark Bieda. For more information: Why use Tamalpais? And other Methods Information To access sample data, go to Sample Data Download Page
Please reference Bieda et al., 2006 Genome Research 16:595 if you use results from this website!

1. Specify 1-3 gff files containing NimbleGen array data ('ratio' files).

These files may be submitted as "raw" gff files or compressed ".zip" files. For compressed files, submit a separate zip for each gff file (to do this: Windows and Mac OS use default compression; for linux use zip not gzip)

2. (OPTIONAL) Indicate genome assembly. This is not used for peak detection, but is only used for doing additional analyses:

3. Optionally enter a prefix for output files (NO SPACES):

4. Enter your e-mail address (results will be sent here):

5. Submit your data:

IMPORTANT: Use a fast internet connection. These files are LARGE.

6. Wait for results to arrive by e-mail (approx 20 minutes).

Important Note on Data Privacy: We will not use your data in any way unless your file generates errors, and you will be informed of this in the rare event that it happens.