Host-bacteria Correlation analysis
Hi,
I have OTU table.txt where every cell contains a percentage and the table is divided into three cell type IL, TR and RE and the for each cell type it would be divided into the 6 Taxonomic levels (Class Family Genus Order Phylum Species). Furthermore for every level I have the three different amplicion (v1v2 v3v4 v5v6). I also have BED/bim/fam files. How I can perform correlation analysis and extract SNPs related to bacteria????? I have already installed PLINK.
Thank you
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
SQL request from NCBI metadata and stat_analysis tables
written by marie.harmel •
-
Rarefaction curve of microbiome study
written by aea55647 •
-
Normalizing RNA read counts for each gene?
written by pearl2070 •
-
Renaming column of taxonomic annotation file
written by bionix •
-
OTU Table Extraction from Phyloseq Object
written by safiq713 •
-
Making a network of Microbiome abundance data and Metabolome data
written by lorenzo.campanelli11 •
-
How to fix Error in `$<-.data.frame`(`*tmp*`, "Kingdom", value = character(0)) : replacement has …
written by arsilan324
-
Extract the 'phylum' and 'species' under "classification" using Taxize package in R
written by horsedog •
-
PCOA plot for special genus
written by agata88
-
Scan Through Txt, Append Certain Data To An Empty List In Python
written by hicsuntdrac0nis •
I found a nice tutorial all R based for GWAS, I hope I could adapt this for my question too
http://www.stat-gen.org/tut/tut_intro.html