Hello, I was wondering if when mapping two data sets on two different Galaxy servers, since the size of the generated BAM files would exceed the quota of the main server, then there is the option of using the data from one server to another to generate the matrix of counts that I will need for my differential expression analysis
Yes, you could generate BAM → counts at both servers, then combine those reduced count sample files together at one for downstream steps. Make sure any reference data incorporated is exactly the same at both.
How to move data around between servers: Transfer entire histories from one Galaxy server to another
If you are an academic researcher (edu email address, or similar), you can also also request a temporary quota grant at many public Galaxy servers. Do this by contacting the admins of the server, and some have a request form on the homepage.
Thank you for ypur help @jennaj 
1 Like