Hi guys I am really sorry to bother you to help me on this! I am following a tutorial that I am almost finishing but I got to understand what its going on. I have a csv like this:
$>cat UHR_vs_HBR.csv "ids","type","path" "UHR_Rep1","UHR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/UHR_Rep1" "UHR_Rep2","UHR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/UHR_Rep2" "UHR_Rep3","UHR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/UHR_Rep3" "HBR_Rep1","HBR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/HBR_Rep1" "HBR_Rep2","HBR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/HBR_Rep2" "HBR_Rep3","HBR"," /media/paulo/44691167-b916-42ad-87f0-b215c6ef2e6c/paulo/bioinfo/griffithlab/RNAseq_Bioinformatics/RNA_DIR/expression/stringtie/ref_only/HBR_Rep3"
This csv has the fullpath to the dir(HBR and UHR samples) where are located each of the samples files :
The R script is this one: enter link description here
But at the start i got this error:
Error in ballgown(samples = as.vector(pheno_data$path), pData = pheno_data) : Something is wrong: are you missing .ctab files? Do extra files/folders (other than tablemaker output folders) match your samples/dataDir/samplePattern argument(s)?
I know that my paths are very weird but I forgot to adjust my Ubuntu installation 8) so... I know that ballgown is complaining about reading the folders and the files in them.
Do you see something I didn't? PS- any other code works with these ugly full paths.
Thank you all! Paulo
Hey Guys I tried to clean the space typo, put some others ' " ' that were missing, but still complaining. 8(
Error in ballgown(samples = as.vector(pheno_data$path), pData = pheno_data) : must provide either "samples" or both "dataDir" and "samplePattern"
I will try to make that file again.
I will let you know.
Thanks to all!
I change the samples to a dir ballgown and make the file with paths again and its working!
Thanks to all!