Bioinformatics Asked by fatima on December 3, 2020
I am trying to reproduce the work of this paper
[1], and I have run StringTie successfully, but after that I have to run Ballgown but could not understand this command:
>pheno_data = read.csv("geuvadis_phenodata.csv")
Actually, I dont know how to make the .csv file of my samples. What phenotype information should this csv contain?
I have checked the supplementary data of this research article but didn’t find any .csv file.
How I can make the .csv file for my samples to load the phenotype data for ballgown?
Load the phenotype data for the samples. An example file called
geuvadis_phenodata.csv is included with the data files for this protocol
(ChrX_data). In general, you will have to create this file yourself. It contains
information about your RNA sequencing samples, formatted as illustrated in
this csv (comma-separated values) file. Each sample should be described on
one row of the file and each column should contain one variable. To read this
file into R we use the command read.csv. In this file the values are
separated by commas, but if the file were tabdelimited you could use the
function read.table.pheno_data = read.csv(“geuvadis_phenodata.csv”)
You can easily do it via Notepad++ or even Excel. Just don't forget to save the output file as a .csv
file (comma-separated value).
The info inside should look like (my working example):
id,state
lar_control141,control
lar_control142,control
lar_control143,control
lar_probiotic142,probiotic
lar_probiotic143,probiotic
lar_probiotic144,probiotic
lar_probiotic145,probiotic
lar_probiotic146,probiotic
That should work
Answered by Dmitrii Trubetskoy on December 3, 2020
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