Germinal center trajectories and transcriptional signatures define CLL subtypes and their functional regulators

This repository contains the RNA sequeuncing data analysis pipeline used in the paper "Germinal center trajectories and transcriptional signatures define CLL subtypes and their functional regulators" Alignment: Contains the code used to align and quantify the sequencing data and its outputs. Each subfolder refers to a specific dataset which are processed with nf-core/rnaseq pipeline with the important intermediary files such as fastqc, multiqc (quallity control), pipeline_info and start_salmon (quantification). Analysis: Contains the code to analyse the counts produced with the nf-core pipeline.The scripts are ordered based on order of execution (Op1, Op2, Op3 then Op4).The scripts take inputs from the proper folders, describe the analysis workflow and saves results to the designated output folders. Attention: File paths must be adjusted in all the script to run correctly.