deepTools offers multiple methods for highly-customizable data visualization that immensely aid hypothesis generation and data interpretation. It also offers all the tools needed to create coverage files in standard bedGraph and bigWig file formats allowing various normalization procedures and comparisons between two files (for example, treatment and control).
See this NAR supplement.
|storage (directly attached)||2 TB|
|Galaxy Performance Settings|
|CPU cores per job||6|
|concurrent jobs per user||1|
|queueing system||Galaxy built-in|
|Exemplary run time|
|BAM file||170 M reads|
|BED file||10000 regions|
- deepTools entry in the Public Galaxy Server list
- deepTools home page at GitHub
- Fidel Ramírez, Friederike Dündar, Sarah Diehl, Björn A. Grüning, and Thomas Manke. deepTools: a flexible platform for exploring deep-sequencing data Nucl. Acids Res. first published online May 5, 2014 doi:10.1093/nar/gku365
- deepTools: a flexible platform for exploring deep-sequencing data presentation by Sarah Diehl at GCC2014