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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?

  1. 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")


  1. Pertea et al, Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown, Nature Protocols volume 11, pages 1650–1667 (2016)
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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

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