Running Nucleosome Dynamics Workflow
Nucleosome Dynamics tools are inter-operable parts that conforms a complete analysis pipeline. With Galaxy, you can combine these tools to create the analysis pipeline that better suits your needs.
At ELIXIR-ES galaxy server, a complete workflow running 'Nucleosome Dynamics' tool and the rest of nucleosome-related analyses is offered. The primary data is the pair of MNase-seq datasets to be compared (BAM format). For each, the nucleosome caller will be execute, and the resulting nucleosome positions will feed into 'Nucleosome Dynamics'. Additionally, the rest of the toolkit analyses and statistics will be computed.
- Select Nucleosome Dynamics Workflow from the toolbar at the left side.
Before running any workflow, remember that you need to be logged. If not, you won't have access to published workflows or generate a new one.
- Configure the workflow by setting the input file and the arguments for each workflow step.
At step 1 and 2 (readBAM tool), your MNase-seq reads are to be selected. Make sure you have them imported in your history (read the previous section to learn how to do so). Also notice that the type of library (paired/single) is one of the arguments to be filled in. Check the rest of the steps to make sure that the argument's default values are fine for your run. Finally, click 'Run Workflow'.
ℹ️ Learn more about each of the arguments for the analyses at the usage section
- Along the execution, the outputs of all the analyses will be progressively added to your history as the step executions are completed.
Force "refresh" to update the history items to make sure the outputs are displayed.
The list of expected files are:
- nucleR
- 2: NR__.gff
- 2: NR__.gff
ℹ️ Learn more about each of the results at the results section
