Notebook Daniel S. Standage

NCBI's Sequence Read Archive is the go-to repository for published genome-scale sequence data sets. Although there are a variety of ways to download sequence data from SRA, the fastq-dump command from the SRA Toolkit is the most convenient in my opinion. In fact, with a few settings tweaks fastq-dump can stream data directly from the SRA into an analysis pipeline …

In which I briefly motivate the utility of generator functions and demonstrate that they can be nested to create a data processing stream.

In which I ramble on about experimental science, research software, and cyberinfrastructure engineering.

I am on my way home from a workshop on cyberinfrastructure and postgraduate training hosted by the Plant Science Research Network. It was a grueling three-day sprint, but it brought together a phenomenal diversity of experience and perspectives on the relevant issues. I wanted to summarize my thoughts while they are still fresh in my head. Beware: what follows is …

tl;dr? It's fine, just ignore secondary/supplementary alignments and don't disable reporting of unaligned reads.

This morning I read On genomic repeats and reproducibility by Can Firtina and Can Alkan. The paper discusses two notable observations regarding calling genomic variants.

1. Some sequence read aligners are not deterministic, and shuffling the order of the reads can result in different alignments.
2. Some variant callers are not deterministic, and will report a different set of variants if an …

Last night I started a batch job on our group's cluster to download and process 9 Illumina libraries from the NCBI SRA. In the past, I have almost always downloaded such data via direct links to .sra files on the SRA FTP site, and then converted these files to Fastq format using the fastq-dump command from the SRA Toolkit. However …

My affiliation recently changed from Indiana University to UC Davis, and accordingly my IU credentials no longer give me access to the eduroam wifi network. Over the last couple of days I've been struggling to connect my laptop to eduroam using my new UC Davis credentials. At first I thought the it was an issue with my account, but it …

Summary of interesting reads over the last several months.

I created a table for my iLocus paper tonight, and wanted to capture the commands used to populate it while everything is still fresh in my mind.