The role of a mammalian network in regulating ischemic stroke outcome

<p>QUICK GUIDE ABOUT THE FOLDERS AND FILES</p> <p>This repository contains the code used to align the sequences and to analyse the counts used in the paper: The role of a mammalian network in regulating ischemic stroke outcome. Plus, it has intermediary files regarding steps of data processing. For example, the output files produced with fastqc, multiqc, PCA and other methods. The raw fastq files of the aligned sequences can be downloaded from GEO database using the links provided in the publication.</p> <p>"Alignments" folder contains the code used to align and quantify the sequencing data.&nbsp;<br>Each subfolder is associated to a specific sequencing dataset used in the paper.<br>For miRNA and total RNA sequences, we used the corresponding nf-core pipeline.<br>For circular sequences, we used ciriquant software pulled into a local docker.<br>For each run of nf-core pipeline and ciriquant, we kept the most important intermediary files like the ones related to quality control from "fastqc" and "multiqc".<br>For each run of nf-core pipeline, the subfolder "pipeline_info" contains the report of the execution of the nf-core pipeline and the command used to call it.<br>For ciriquant run, config.yml and op0_CIRIquant.sh show which has been the setting and files used for the execution.<br>The alignment of total RNA sequencing data has been performed twice.<br>Standard alignment with default parameters.<br>Edited_genome alignment with the mm10 genome annotation modified to include Cdr1as.<br>Mus_musculus folder contains the mm10 genome annotation modified to include Cdr1as.</p> <p>"Analysis" folder contains the code to analyse the counts produced with the nf-core and ciriquant pipelines.<br>Each subfolder is associated to a specific sequencing dataset used in the paper.<br>The scripts of a folder are always indipendent from the files belonging to other folders.<br>The scripts are ordered based on how they must be executed, so op1, op2, op3 ...<br>The scripts always elaborate the data coming from their "data" folder, use the functions inside their own "funs" folder and produce the results in their own "output" folder; changing the structure of a folder may give errors during the execution of a script.</p> <p>"Analysis_revision" folder contains the code to add to the "Analysis" folder.<br>This code has been added to reply to reviewer's comments.</p> <p>BE CAREFULL: both the code for the alignments and analysis includes pointers to file paths which must be changed in order to be run in your system.</p>