I am working on RNA-Seq dataset that consists of two conditions- Control and Sample. My goal is to get differentially expressed genes between the two conditions, for which I am using ballgown package on R. My concern is when I try to load the control and samples onto a single ballgown object for DE analysis, it shows an error-
Error: intron ids were either not the same or not in the same order across samples. double check i_data.ctab for each sample.
The object isn't able to load since the IDs are different. Same is the case with exons and transcripts ids. Upon looking into the .ctab files, the exons, introns, transcripts differ across Control- Sample. But are same across the 3 controls. And they are same across the 5 samples. It is like so- Controls: exon 442247, introns 366654, transcripts 181466. Samples: exon 686514, introns 416565, transcripts 247538. The exons, introns, transcripts differ only between the two conditions. Hence, I am not able to progress from here. Can anyone please help me with as to why this is occuring? Why would the exons, introns, transcripts id be different for control & sample, since both control and sample RNA are collected from human patients. Please add a note on how I can solve this issue.
Any help is much appreciated.