Mouse Genomics

This repository contains code to help with the setup of a Genomics cluster without root privilages. The information detailed here, as the name implies, is oriented to Mouse Genomics. Thus, most scripts will be downloading mouse data from Ensembl, UCSC or NCBI.

Software set up should be generic, though check to make sure you are downloading appropriate reference files for you own species of interest (not everyone is interested in humans). Pay special attention to the $PATH where things are located and that you're not deleting something important.

Analysis pipelines will most likely need to be adapted to your own style and data structure. Though... take the ideas and best of luck with your work !

custom file extension

<>.slq : SLURM sbatch file

<>.Rtxt : R session transcript, not a script

<>.awk : awk command

Directories/

DNAseq/

Contains scripts for the mapping and alignment of DNA high throughput sequencing data using bwa. In addition it contains script for variant calling using four pipelines

1. GATK using HaplotypeCaller and VQSR

2. Freebayes

3. Platypus

4. SAMtools mpileup | bcftools call

RNAseq/

Contains scripts for the mapping and alignment of RNA high throughput sequencing data using STAR aligner and TopHat. In addition it contains scripts for counting and quality assesment of the RNA sequences.

QTLMapping/

Contains scripts for QTL mapping in mouse inbred strains.

GeneExpression/

Contains scripts for the analysis of gene expression data.

Scripts

create.igenome.sh

This script creates an iGenome « LIKE » reference genome. The iGenomes are Illumina's bundled referece and annotation packages to be used with GenomeStudio. an iGenome has the following simplified directory tree structure

Mus_musculus/                                                     ## Organisms/species
└── Ensembl                                                       ## Format/Data source
    ├── Grcm38                                                    ## Reference Genome release
    │   ├── Annotation                                            ## Feature annotation file
    │   │   ├── Genes
    │   │   │   └── genes.gtf, refFlat.txt, refGene.txt           ## gene annotation files
    │   │   ├── SmallRNA
    │   │   │   └── mature.fa precursor.fa                        ## Fasta files from miRBase
    │   │   └── Variation
    │   │       └── Mus_musculus.gvf, Mus_musculus.vcf            ## Genomic variation
    │   └── Sequence
    │       ├── AbundantSequences                                 ## fasta files
    │       │   └── adapter_contam1.fa* MT.fa* musRibosomal.fa*
    |       |       phix.fa* polyA.fa* polyC.fa*                  ## * refers to .fa.2bpb and .fa.vld index
    │       ├── Bowtie2Index
    │       │   └── genome.*.bt2 genome.fa -> ../path/to/ref      ## Bowtie2 indexes and link to genome.fa
    │       ├── BowtieIndex
    │       │   └── genome.*.ebwt genome.fa -> ../path/to/ref     ## Bowtie1 indexes and link to genome.fa
    │       ├── BWAIndex
    │       │   └── genome.fa.* genome.fa -> ../path/to/ref       ## BWA indexes and link to genome.fa
    │       ├── Chromosomes
    │       │   └── 1.fa ... 19.fa X.fa Y.fa MT.fa                ## Fasta files from individual chromosomes
    │       ├── Squashed-Mus_musculus-Ensembl-Grcm38
    └──     └── WholeGenomeFasta
            └── genome.fa genome.fa.fai genome.dict               ## Genome Reference in Fasta, samtools faidx
                                                                  ## and picard CreateGenomeDictionary.jar 
                                                                  ## index files

The directory structured is simplified as in addition to Annotation and Sequence, directories, there is an additional GenomeStudio which contains symbolic to the appropriate locations, and each directory has an Archives or versionXX directory where the data is contained and then sym-linked to the files shown here. The symbolic link strategy was not reconstructed, however, the essence of the data structure was preserved in this script shuch that it resembles the above. The location and additional README files will be downloaded along with the data for reference.

envar.sh

Contains a collection of environment variables that are used in many scripts.

setup_bin.sh

This script goes through an src/ directory, finds all executable files and sym-links them to a $HOME/bin. The script is convinient when working as a user in a High-Performace Computing cluter. It helps to keep all your latest programs in the src/ but still be able to access it withouth specifying the entire path/to/src/dev-src-git-clone/bin/MyAwsomeTool. Note: $HOME/bin must be in the $PATH.

setup_genomicscore.sh

This script downloads the source code of about 14 programs useful for Highthrougput sequencing. After running this script, the setup_bin.sh will generate your $HOME/bin

sort.igenome.sh

This script goes through the annotation files and fasta files and performs a version sort sort -V. Genomics tools such as bwa, Tophat, Cufflinks, STAR, SAMtools, vcftools, etc like to have everything in the same order, hence the script.