My post will probably look "basic" to many of you but either, let's go. I am really beginner (I have the foundations of the modules available via Coursera) so my terminology may be incorrect.
I have to analyze RNA-seq data in order to arrive at the top differentially expressed genes between my samples disease/health. The analyst who was in charge of performing the RNA-seq with my samples is going to reads alignment and sent me data aligned in .bed .bam and .bai format.
When i look for analysis tools I know that I must proceed to the assembly, then the quantification of the expression of the transcripts to arrive at the differential splicing and expression. I found a huge amount of tools, commands, environments to use but it's still nebulous to me. So I wanted to use Galaxy (Cufflinks-> cuffmerge-> Cuffdiff) to get my results but apparently my files are too heavy for this tool :/ Would anyone have suggestions of pipelines, worflow or even better tools / environment that are better than others to analyze this type of data? or that are used in routine in analysis? Every suggestion or advice is welcome.
Thank you very much for your help.