Functions/scripts used in the AID.cry UPD-Seq publication
Step1: Do the Sequence alignment and create .bam files
Step2: use GCmmDepth to extract depth of coverage after applying the GCmm Filter
Step3: Calculate Differential Coverage using the NDC2 fuction
Step4: Find peaks using a threshold (5x the standard deviation of NDC output)
Step5: Extract nucleotide counts as described here: https://github.com/rayanramin/U-idx#readme
Step6: Calculate UI using the UX.R function and perform the Analysis (follow UI/UI Analysis)
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If you need help or have any questions regarding the code,
please contact the corresponding author or Ramin Sakhtemani:
rsakhtemani (at) mgh.harvard.edu
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