From ef3b7cf1499c4d9473bd58238ce9d143013a77e6 Mon Sep 17 00:00:00 2001 From: Zoey Werbin Date: Mon, 8 Mar 2021 14:54:24 -0500 Subject: [PATCH] Update README.md --- README.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/README.md b/README.md index 30ad065..c44cc00 100644 --- a/README.md +++ b/README.md @@ -1,10 +1,10 @@ # metagenomes_NEON -This repository contains code for downloading and processing shotgun metagenomics data from the National Ecological Observatory Network (NEON). This accompanies a tutorial for processing the raw reads. +This repository contains code for downloading and processing shotgun metagenomics data from the National Ecological Observatory Network (NEON). This accompanies a tutorial for processing the raw reads, accessible on F1000 Research. -Two BLAST analyses are included in the tutorial: one focuses on N-cycling genes, and the other on antibiotic resistance genes. There are scripts here for parsing the BLAST output (in Python), writing it to a CSV file, then visualizing the results in R. +Two BLAST analyses are described in the tutorial: one focuses on N-cycling genes, and the other on antibiotic resistance genes. There is an example script here for parsing the BLAST output (in Python) and writing it to a CSV file, `blast_parser.py`. Then, the scripts beginning with `normalize_gene_counts` can be used to normalize data using the DeSeq R package and visualize the results in R. -To recreate or update `metadata_metagenome.csv` (the file with raw NEON sample read counts), run this code in R (takes < 3 minutes): +To update `metadata_metagenome.csv` (the file with raw NEON sample read counts - necessary for normalization), run this code in R (takes < 3 minutes): ``` library(neonUtilities)