How-to
Short tutorials on genomic and transcriptomic analyses.
Downloading data download data from SRA
download data from gemma
Aligning …
How-to: align DNA-seq data
Aligning with BWA References: https://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_li.pdf …
How-to: align RNA-seq data
Aligning with STAR Get the latest version of STAR. All things STAR here: https://github.com/alexdobin/STAR.
Precompiled binaries are …
How-to: build co-expression networks
Gene expression profiles that co-vary suggest co-regulation, co-function or co-localization. This pipeline involves the construction of …
How-to: build the gene ontology
Get ontology and annotation files wget http://purl.obolibrary.org/obo/go.obo wget …
How-to: call variants from DNA-seq data
https://software.broadinstitute.org/gatk/documentation/quickstart https://software.broadinstitute.org/gatk/download/ …
How-to: call variants from RNA-seq data
https://software.broadinstitute.org/gatk/best-practices/workflow?id=11164
Install GATK4 Download the precompiled jar binaries. Set …
How-to: download data from SRA
References: https://www.michaelgerth.net/news--blog/how-to-efficiently-bulk-download-ngs-data-from-sequence-read-databases
Using SRA …