I'm currently trying to generate pileup files for a gene from sra archives of many RNA-seq experiments. At the moment, regardless of the parameters entered, I am always returned an entirely empty file - no error, it just says that the job is finished.
I've managed to generate FASTQ files from these same archives so I know there's data there. I've tried all possible ways of selecting my gene of interest, including leaving the aligned region blank. All give me the same, blank output.
I'd be grateful for any suggestions of how to extract a pileup file from sra, either using this tool or alternatives!