Ballgown error

[keets9]

Hi

I ran this command:

bg_sample = ballgown(dataDir="Ballgown", samplePattern= "SRR", pData=pheno_data)

Then i got the below error, during intron merge,

### ### Error in ballgown(samples = c(... : intron ids were either not the same or not in the same order across samples. double check i_data.ctab for each sample.

kindly help, thank you
keets

[alyssafrazee]

Hello! This example isn't reproducible, since there's no way to see what data you're attempting to read or from where. For more help, could you please provide the following info?

1. the full file path to your ballgown data (what's your top-level folder named and what are the names of all your subfolders)
2. the first few lines of the i_data.ctab files for 2-3 of your samples
3. the contents of pheno_data (is it a data frame? file path?)

[keets9]

1. Full path to ballgown:

#loading the data
sample_data=read.csv("E:/hisat2-2.2.0/ballgown/sample_data.csv")
#readng the expressiondata calculated by stringtie(ie the ballgown files)
SRR_bg=ballgown(dataDir = "E:/hisat2-2.2.0/ballgown",samplePattern = "SRR",pData = sample_data)
2. Ctab files
sample1:
i_id chr strand start end rcount ucount mrcount
1 1 + 12228 12612 0 0 0.00
2 1 + 12722 13220 0 0 0.00
3 1 + 12058 12178 0 0 0.00
4 1 + 12698 12974 0 0 0.00
5 1 + 13053 13220 0 0 0.00
6 1 + 13375 13452 0 0 0.00
7 1 - 14502 15004 0 0 0.00

sample2:
i_id chr strand start end rcount ucount mrcount
1 1 + 12228 12612 0 0 0.00
2 1 + 12722 13220 0 0 0.00
3 1 + 12058 12178 0 0 0.00
4 1 + 12698 12974 0 0 0.00
5 1 + 13053 13220 0 0 0.00
6 1 + 13375 13452 0 0 0.00
7 1 - 14502 15004 0 0 0.00
8 1 - 15039 15795 0 0 0.00
sample3:
i_id chr strand start end rcount ucount mrcount
1 1 + 12228 12612 0 0 0.00
2 1 + 12722 13220 0 0 0.00
3 1 + 12058 12178 0 0 0.00
4 1 + 12698 12974 0 0 0.00
5 1 + 13053 13220 0 0 0.00
6 1 + 13375 13452 0 0 0.00
7 1 - 14502 15004 0 0 0.00
8 1 - 15039 15795 0 0 0.00

3 contents of pheno data

sample	sampletype
SRR60551202	Tumor
SRR60551203	Tumor
SRR60551204	Tumor
SRR60551205	Tumor
SRR60551206	Tumor
SRR60551207	Tumor
SRR60551208	Tumor
SRR60551209	normal
SRR60551210	normal
SRR60551211	normal

[keets9]

the CSV file was taken into data frame.

[ArpanPrj]

I am getting similar issue. Can anyone tell me how to solve this?