Here you can find all the scripts to reproduce the analyses performed in Rouco et al. 2024 "Temporal constraints on enhancer usage shape the regulation of limb gene transcription".
Each directory contains the specific command lines used for each analysis.
ChIP-seq and RNA-seq pipelines were adapted from lldelisle repository: https://github.com/lldelisle/myNGSanalysis/
As the Early Late putative enhancers classification on entire forelimb datasets was performed by combining RNA-seq and ChIP-seq output datasets. The analysis performed after generating the FPKM, Count and narrowpeak output files is presented in a separate folder Early_Late_putative_enhancers_classification_entire_forelimb