Harmon’s public notebook

Comparing fragment length and duplication analysis between BBtools and Bowtie2

An application of the v2.4.0 pipeline on Crits-Christoph 2021

We’d like to thank Mike for his contributions in helping us understand how to conduct the duplication and fragment length analyses. This analysis was based of an example…

Harmon Bhasin, Will Bradshaw

Workflow of Aydillo et al. (2022)

Whole blood from US (RNA)

This is the third and last whole blood study of this series. In this post, I analyze Aydillo 2022, a dataset with 53 healthy individuals in the USA.

Workflow of Thompson et al. (2023)

Individual whole blood from US (RNA)

This is another potential study of this series. In this post, I analyze Thompson 2023, a dataset with 417 samples of whole blood from healthy and SARS-CoV-2 infected…

Workflow of O’Connell et al. (2023)

Whole blood from US (RNA)

This is the first whole blood study of this series. In this post, I analyze O’Connell 2023, a dataset with 138 adult whole blood donors from Austin, TX.

Workflow of Mengyi et al. (2023)

Pooled plasma from China (DNA)

This one of the studies that we hope to discuss in our third blog post, which will cover the metagenomic analysis of whole blood/plasma. In this notebook, I analyze Mengyi…

Workflow of Thijssen et al. (2023)

Pooled plasma from Iran (DNA + RNA)

This is another potential study of this series. In this post, I analyze Thijssen 2023, a dataset with 20 pooled samples from 100 healthy individuals in Iran.

Workflow of Cebria-Mendoza et al. (2021)

Pooled plasma from Spain (DNA + RNA)

As a part of my time here, I’m exploring blood-based surveillance for novel viral pathogen detection. We’ve decided to make three blog posts. The first blog post will cover…