Questions about ChIP-Seq methods for bake-off

(Please feel free to add any other questions that would be helpful for the software comparison.)

1. What version of your software was used?
2. What inputs/parameters are
   • required?
   • optional?
3. What formats of mapped reads are allowed? Is any other information about genome required?
4. Can mapping data include tags that were mapped to >1 location? If so, how are these multiple mappings handled?
5. Can replicate Seq samples be processed as such? If so, how are they used?
6. Is there scaling of datasets with different numbers of tags? How?
7. Is there smoothing/extension of tags and/or counts? How?
8. How were peaks selected and ranked?
9. How was control data used?
10. What statistical distribution is used to model the distribution of tags along the genome?
11. If statistics (p-values) are calculated, how is this done?
12. Is the program run any differently depending on the expected width of a typical binding region?
13. How would you describe the ease of use of the software for
    • bioinformatics people?
    • biologists?
14. Are forward and reverse reads used differently? Are they used to narrow the binding point?
15. How are tags mapping to the same position treated?