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Short tutorials on genomic and transcriptomic analyses. Downloading data download data from SRA download data from gemma Aligning RNA-seq align RNA-seq data align DNA-seq data Variant calling call variants from DNA-seq data

Aligning with BWA References: https://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_li.pdf https://genomics.sschmeier.com/ngs-mapping/#mapping-statistics Get BWA http://sourceforge.net/projects/bio-bwa/files/ http://bio-bwa.sourceforge.net/bwa.shtml bunzip2 bwa-0.X.X.tar.bz2 tar xvf bwa-0.X.X.tar cd bwa-0.X.X make export PATH=$PATH:/path/to/bwa-0.X.X source ~/.bashrc Download data Reference genome wget ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_31/GRCh38.p12.genome.fa.gz Index genome bwa index -a bwtsw GRCh38.

Aligning with STAR Get the latest version of STAR. All things STAR here: https://github.com/alexdobin/STAR. Precompiled binaries are easiest. wget https://github.com/alexdobin/STAR/blob/master/bin/Linux_x86_64_static/STAR Or you can compile from source. # from latest release wget https://github.

Genotypes Create a personal genome Use the reference genome With a genotype Without a genotype Mapping See the RNA-seq alignment page. Counting Assessing

Gene expression profiles that co-vary suggest co-regulation, co-function or co-localization. This pipeline involves the construction of individual gene co-expression networks, the aggregation of these networks, and then an assessment via neighbor-voting.

Get ontology and annotation files wget http://purl.obolibrary.org/obo/go.obo wget http://geneontology.org/gene-associations/goa_human.gaf.gz Other species annotations (ontology is the same) wget http://geneontology.org/gene-associations/gene_association.sgd.gz wget http://geneontology.org/gene-associations/gene_association.mgi.gz Get gene info files to convert between IDs wget ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene_info.gz Make gene id to name file, for each species zcat gene_info.

https://software.broadinstitute.org/gatk/documentation/quickstart https://software.broadinstitute.org/gatk/download/ https://software.broadinstitute.org/gatk/best-practices/ Install GATK4 Download the precompiled jar binaries. Set paths. Running GATK gatk HaplotypeCaller \ -R genome.fa \ -I sample.sort.dedup.realign.bam \ -O sample.raw_variants.vcf Or gatk HaplotypeCaller \ -R genome.

https://software.broadinstitute.org/gatk/best-practices/workflow?id=11164 Install GATK4 Download the precompiled jar binaries. Set paths. Adding read groups to bam file java -jar picard AddOrReplaceReadGroups \ I=sample.filt.bam \ O=sample.rg.bam \ SO=coordinate RGID=id RGLB=library RGPL=platform RGPU=machine RGSM=sample Marking duplicates java -jar picard MarkDuplicates \ I=sample.

https://www.ncbi.nlm.nih.gov/pubmed/22782548 https://gemma.msl.ubc.ca/home.html https://github.com/PavlidisLab/gemmaAPI.R Install the wrapper library(devtools) devtools::install_github('PavlidisLab/gemmaAPI.R') Download data data = datasetInfo('GSE19804', request='data', filter = TRUE, return = TRUE, file = NULL ) Get metadata meta = compileMetadata('GSE19804', outputType = "list")

Install the wrapper library(GEOQuery) Download data