seqmonk.txt

# Groups
* Data Groups: technical replicates (same cell)
* Replicates sets: biological replicates (same tissue)

# Strands
* Red strand: left -> right (top) +
* Blue strand: right -> left (bottom) -

# Quantification pipelines
* Read count quantifications: How many reads overlap with probe
* Base pair quantifications: How many base pairs of read overlap with probe
* Enrichment quantifications: How many more reads overlap with probe than
  expected by chance
* Difference quantification: Difference strands
* Coverage quantification: Which % of the probe is covered
* Coverage depth quantification: Overlap of reads within probe

# Plots
* Probe value histogram
* Box Whiskerplot
* Scatterplot
* Probe trend plot: distribution quantification within all probes
* Aligned probes plot: distribution quantification within individual probes


# Filters
* Does not depend

* Filter on values -> Individual probes: >= 0 // remove NA
* Statistical tests -> BoxWisker: outliers Boxplot
* Statistical tests -> Windowed Replicate (probes overlapping feature)
  * 1 probe: do probes in window deviate from value?
  * 2 probes: t-test
  * >2 probes: ANOVA
* Statistical tests -> Replicate set: Like windowed for replicates (>3 required)
* Filter by position: (Current) position
* Filter by probe length: if probes haves different length, e.g. genes
* Filter by features: probes must be (in) feature
* Combine existing list: combine different filters
* Right click ->
  View list: export as txt