Posts

Short tutorials on genomic and transcriptomic analyses. Downloading data download data from SRA download data from gemma Aligning …

Aligning with BWA References: https://www.broadinstitute.org/files/shared/mpg/nextgen2010/nextgen_li.pdf …

Aligning with STAR Get the latest version of STAR. All things STAR here: https://github.com/alexdobin/STAR. Precompiled binaries are …

Gene expression profiles that co-vary suggest co-regulation, co-function or co-localization. This pipeline involves the construction of …

Get ontology and annotation files wget http://purl.obolibrary.org/obo/go.obo wget …

https://software.broadinstitute.org/gatk/documentation/quickstart https://software.broadinstitute.org/gatk/download/ …

https://software.broadinstitute.org/gatk/best-practices/workflow?id=11164 Install GATK4 Download the precompiled jar binaries. Set …

References: https://www.michaelgerth.net/news--blog/how-to-efficiently-bulk-download-ngs-data-from-sequence-read-databases Using SRA …