I have an ran seq experiment -paired end, 100 bp, where I am trying to compare control vs test samples. I am using a Xenopus Laevis genome (Xenbase v9.1) which I uploaded via FTP. I uploaded the data sets, trimmed them and then aligned them with TOPHAT tool to my 'custom genome from history'.
When I took the course, at this point we looked at the data but we were using a human genome that was available and there was a link in the TOPHAT accepted hits to USCU main. My genome is not there so there is no such link and now I'm lost. I would just like to compare the data sets to see if there is anything in the test which is not in the control. Thank you