The development and implementation of our CAGE-seq pipeline was done in R version 4.1., bioconductor(latest) and using ORFik as one of the base packages. To run CAGE-pipeline, run below command in terminal.
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To setup folder structure, use below mentioned scripts with the arguments in same sequence. Rscript construct_folder_struct.R
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To move raw files from local directory or to download from online repo, use below mentioned script. Rscript get_fastq.R <local/Online> <"Path to local file"/"Experiment Accession(primary or secondary)">
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To map raw reads to a genome, use below mwntioned script. Rscript mapping.R <local/Online>
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To reassign TSS of each transcript and generate a simple dataset: Rscript Reassign_TSS.R <Yes/No> <"Path to save transcript data set">