Analysis Modules

First, SQUAT will randomly sample 1M entries of input reads and provide the percentage of poorly-mapped reads based on overall assessment of the alignment experiments. (You can find how the percentage is calculated here)

It goes on to manipulate various analysis modules to get to the nitty-gritty, listed as follows:

• Basic Statistics
• Read Labeling
• Mismatch, Clip, and N Ratio
• Alignment Score