Load phenotype data for samples

Question

[fatimarasool135]

Hi, I am following this paper and i have read many times this paper:

• Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

and I have run strigtie sucessfully, after that I have to run the ballgown but could not understand this command.

pheno_data = read.csv("geuvadis_phenodata.csv")

Actually, I don't know what how to make .csv file of mine samples.what pheno information contain this .csv file.

I have checked the supplementary data of this research article but not found any .csv file.

Please guide me how I can make this .csv file for my samples for step number 8 load the phenotype data for ballgown

Answer 1

[lakhujanivijay]

The file is included in the data provided with the paper and contains the following information:

cat chrX_data/geuvadis_phenodata.csv

"ids","sex","population"
"ERR188044","male","YRI"
"ERR188104","male","YRI"
"ERR188234","female","YRI"
"ERR188245","female","GBR"
"ERR188257","male","GBR"
"ERR188273","female","YRI"
"ERR188337","female","GBR"
"ERR188383","male","GBR"
"ERR188401","male","GBR"
"ERR188428","female","GBR"
"ERR188454","male","YRI"
"ERR204916","female","YRI"

[fatimarasool135]

I have generated the pheno.csv file. kindly could you please tell me I am correct ? I have made this files correct?

cat phenodata.csv

---

ids,cultivars
G1,Batis
G2,Blue_silver
G3,Chakwal_50
G4,Local_White
G5,Syn_22
G6,Uz_11_cwa_8

[Ashastry]

Hi,

Phenotype data file should explain the variables in your samples. Ideally it should either have a "condition" or other variable like "time point" depending on the design of your experiment. If you look at csv file from the data, it is clear that the first column consists of sample name/ID, second column is a variable. Can you explain your experiment design?

[fatimarasool135]

Hi Ashastry I have RNA seq 6 samples. i want to compare the differential expressed genes among these samples.could you please suggest me how to set pheno-data text file