RNA Seq Analysis for Publication: XXX

doi:

Repository Organization and Data Availability:

nextflow_pipeline/ --- Contains the nextflow pipeline for performing the quality control, trimming, mapping, and quantification of transcripts.

deseq2_scripts/ --- Contains the DESeq2 scripts used for outlier detection, differential gene expression analysis, and generating graphs.

deseq2_data/ --- Contains code used to cleanup feature matrix, the cleaned-up up feature matrices, and the metada used in the deseq2 analyses.

singularity/ --- Contains the singularity recipe for the container used in this nextflow pipeline.

count_data/ ---- Contains gene quantification matrix with data for all samples outputed by FeatureCounts

quality_control/ --- Contains quality control report html file and QC data made with MultiQC

Raw Illumina gzipped paired-end data can be found at: The OneDrive policy on my current Institution does not allow me to give access to the data to anyboody with the link. If you would like to access the raw data send me an email at [email protected] or [email protected] and I will promptly grant you access. Note that the data is gzipped, to make it work with the NextFlow pipeline you will first need to unzip it using the command gzip -d * on the directory containing the data.

Singularity container and recipe used for this analyses can be found at: Container

Singularity container can be pulled using command: singularity pull library://bernardo-heberle/default/dcnl_illumina_rna_seq:sha256.07e7e087d436daa71709dd0c48d60d0e3f6e50f2a89d5c7d9adf57ebf6ad136e

Mouse reference genome used: Mouse Reference Genome --- Mus_musculus.GRCm39.dna.primary_assembly.fa.gz

Download from command line: wget ftp.ensembl.org/pub/release-104/fasta/mus_musculus/dna/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz

Mouse reference annotation used: Mouse Genome Annotation --- Mus_musculus.GRCm39.104.gtf.gz

Download from command line: wget ftp.ensembl.org/pub/release-104/gtf/mus_musculus/Mus_musculus.GRCm39.104.gtf.gz

Download this repository using commmand line: git clone https://github.com/bernardo-heberle/dcnl_rna_seq_els_vs_ct