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04/02/2021 - Speaker: Tonia Korves, Ph.D. Lead Data Scientist Data and Human-Centered Solutions Innovation Center MITRE Corporation Abstract As COVID-19 research rapidly escalated last year, we quickly built a platform to help biomedical experts track Read More...

Go back to /data/user/hcc1395_b4b. cd /data/user/hcc1395_b4b Create a directory called hcc1395_featurecounts. mkdir hcc1395_featurecounts Go back into /data/user/hcc1395_b4b/hcc1395_hisat2 for this Read More...

Remember that the deseq2.r script requires that the expression counts table be in csv format. It is currently in tab delimited format as generated by featureCounts. There is also a header line that we Read More...

Let's talk about obtaining expression read counts using an application called featureCounts First let's create a new directory in our ~biostar_class/hbr_uhr folder to store the counts. mkdir hbr_uhr_deg_ Read More...

The module featureCounts from the subread package will be used to quantify gene expression. In the featureCounts command below: -p: specifies the presence of paired end data. --countReadPairs: specifies to count both reads in a Read More...

In this session, participants will practice generating a gene expression matrix for the HBR-UHR data. Sign onto Biowulf and change into the /data/user/hbr_uhr_b4b folder. Solution ssh user@biowulf.nih.gov Read More...

Lesson 15 Practice Objectives Previously, we performed QC on the Golden Snidget RNA sequencing data, aligned the sequencing reads to its genome, and obtained expression counts. We can now finally perform differential expression analysis, to find Read More...

A script allows users to string together analysis steps and keep them in one document. It can be reused with or without modification to analyze similar datasets. The script (SRR23341296_statistics.sh) below will use Read More...

NIH Intramural CryoEM Consortium (NICE) serves intramural investigators in all NIH IC’s. NICE provides access to state-of-the-art Titan Krios cryo-electron microscopes for atomic-resolution structure determination of protein, macromolecular complexes, membrane receptors, cellular organelles, and Read More...

The Biological Products Core provides the AIDS research community with high-quality purified preparations of various strains of Human Immunodeficiency Virus (HIV) and Simian Immunodeficiency Virus (SIV), economically prepared by leveraging the economy of scale. Materials Read More...

[tabby title="Home"] About NICE-NIH Intramural CryoEM Consortium  NIH Intramural CryoEM Consortium (NICE) serves intramural investigators in all NIH IC’s. NICE provides access to state-of-the-art Titan Krios cryo-electron microscopes for atomic-resolution structure determination of Read More...

1. Introduction and Learning Objectives This tutorial has been designed to demonstrate common secondary analysis steps in a scRNA-Seq workflow. We will start with a merged Seurat Object with multiple data layers representing multiple samples that Read More...

Lesson 15: Finding differentially expressed genes Before getting started, remember to be signed on to the DNAnexus GOLD environment. Lesson 14 review In the previous lesson, we learned to visualize RNA sequencing alignment results in the Integrative Read More...

Note that we now have differential expression by transcripts and our first column contains the transcript IDs. But what genes do these transcripts map to? We will need to do some data wrangling to find Read More...

Lesson 16: RNA sequencing review and classification based analysis Before getting started, remember to be signed on to the DNAnexus GOLD environment. Review In the previous classes, we learned about the steps involved in RNA sequencing Read More...