Guidelines

Guidelines to process samples

• Use LSTrAP
• Make sure splice variants are removed, keep a single representative (e.g. the longest transcript) per locus
• Samples must pass default Quality Control
  • Check with scatter plot if default parameters make sense for the current species !
• At least 8M reads need to map unambiguously to coding sequences
• Check for outliers using heatmap/dendrogram

Guidelines to build profiles

Detailed profiles

• Up to 50 conditions can be selected (limit on what can be shown in a graph)
• Duplicates are acceptable for interesting conditions
• Adjacent timepoints of time-series data can be collapsed
• For stress conditions, include the mock treatment for that experiment
• Order samples from lowest tissue (e.g. roots) to top (e.g flowers) where possible
• Select colors consistently

Collapsed profiles

• Tissues should avoid inclusion of stress conditions
• Stress conditions should use non-stressed tissues as background/control !
• Colors should correspond with the detailed profile