All nextflow and nf-core pipelines have been successfully configured for use on the HPC Cluster at New York University. The configuration applies required and recommended options in order to have efficient and reliable nextflow runs. Below is the NYU HPC Read more…
Being rejected from the preprint server, bioRxiv, seemed like a new low for me. But, I was heartened to know that I was in good company. At least an explanation was provided by the bioRxiv team that “every submitted manuscript Read more…
UPDATED: April 16, 2024 nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow. This post will walk you through running the nf-core RNA-Seq workflow. The pipeline uses the STAR aligner by default, and Read more…
During the summer of 2020, the Ghedin and Gresham labs at New York University sequenced several SARS-CoV-2 isolates from clinical samples acquired in New York City. To visualize and share the data among researchers and collaborators we built a JBrowse Read more…
This is an updated version of the variant calling pipeline post published in 2016 (link). This updated version employs GATK4 and is available as a containerized Nextflow script on GitHub. Identifying genomic variants, including single nucleotide polymorphisms (SNPs) and DNA Read more…
In the Kenneth Birnbaum Lab, we are interested in understanding how the plant root is able to grow continuously over the plant’s life and maintain its specific root structure (Fig.1). More specifically, what is the role of the stem cells Read more…
Next-generation sequencing technologies have allowed for sequencing at a low cost and fast speed, and is used more and more to study microbial communities. RNA-seq metatranscriptome and WGS metagenome studies aim to investigate microbial communities at genome and transcriptome levels. Read more…
In this article I’ll go over three Nextflow patterns I frequently use to make development of Nextflow data processing pipelines easier and faster. I use each of these in most of my workflows, so they really come in handy. I Read more…
Comparing HighPrep PCR and AMPureXP for cleanup and size selection Written by Hana Husic High-throughput sequencing requires precise size selection of DNA fragments in order to increase the amount of usable data generated. If the fragments are too small, sequencing Read more…
Gene Set Enrichment Analysis (GSEA) is a common method to analyze RNA-Seq data that determines whether a predefined defined set of genes (for example those in a GO term or KEGG pathway) show statistically significant and concordant differences between two Read more…