chipseq chapter complete review

[rvolckmann]

lot has been changed

[rvolckmann]

• [ ] superenhancer ROSE explanation (new window or tab)

• [ ] update picture 5

• [ ] add TSS graphs within exp text

• [ ] add tss graphs text

• [ ] add TSS genesets scan

• [ ] add TSS XY plot 2 experiments

• [ ] add RSEG Plot

• [ ] add Chipseq TSS Peak/Coverage Plotter

• [ ] Figure 6 including text

• [ ] Select / Adapt chip-experiments has been changed in the left panel from the genome browser has been changed

• [ ] Mention Bernstein dataset at point 4, epigenome road map is also turned on .

[liekeantro]

• [ ] pdf beschikbaar maken voor iedereen

• [x] check mijn gisteren aangemaakte issues

• [x] VERSIE AANPASSENNNN!!!!!

• [x] Step2-7 "Selecting more chipseq experiments" half and delete "Plotting more experiments with tracks".

• [x] Text/ my own understanding: I am not sure what epigenetic information is shown by the NIH roadmap: I know the different colors stand for different tissues, but which exact epigenetic information is it? Same question with the z-scores: zscores of which values?

• [x] Text: Is it correct that the link to the zooming and panning in step 2 should be chapter 17, not 16?

• [x] Text: In step 3 we say that a commonly used value is 50kb up and downstream and therefore we put 100000 as a value; but in the plotter it is not 500002 but 1000002 ; should we adapt step3-2 to fill in 50000 as a distance? Or we have to adapt the 50kb up and downstream, also in step 3-3.

• [x] Figure at step4-5 how did you get the sliding median? Without that the range value is better not adapted, but sounds like a cool feature indeed to be mentioned :)

[jankoster]

If you are describing all the 'settings' that can be adapted when you are within the genome browser, it may be nice to note that a specific view can also be stored as a profile (and be retrieved later on / can function as a template to wander on the genome using the stored settings)

[liekeantro]

Added Jan's remark at the end of the chapter.