I am looking to perform a cumulative analysis of data from multiple RNASeq studies deposited online. Some of the studies uploaded the raw fastq files, but others only upload a post raw mapping counts table or normalized counts ex) https://zenodo.org/record/4114617

I do not have the computing power to perform the same HISAT2 alignment for the other studies raw fastq to compare (normally use salmon). There is an additional in study I want to compare to that uses a third alignment method and only uploaded a raw mapped table.

My end questions are can I compare these different mapping methods on any level and account for it statistically? I know I can run hisat2 and let it run for ~1 week + but I would lose the third group even if possible.

Finally, assuming I ran a hisat2 alignment and quantification from the raw fastq files of study 1 to compare to the hisat of study 2, would I be to compare or swap the controls of each study? The reason is many of these “controls” aren’t true controls and am interested in determining control sample variability.

Thanks,

Luke