I am trying to run tximport on transcript TPM files from sailfish. This problem is that my files are not organised as they are in the Vignette with the quant.sf file for each sample in a separate folder. Instead they had all been combined into one file with separate column for sample.
I have managed to extract the quant data for each sample into a separate file for each however when I try and use those as input I get the message:
I understand this means the data are not organised in the way tximport wants but its difficult to tell what exactly is the problem without understanding the expected input requirements and these are not made clear in the Vignette.
It would be useful if there was a way to input all the quant.sf files in a different way and some guidance how that should look would be helpful for those of use not super proficient at R