Hi! I am new to Galaxy and just received a RNA-Seq dataset generated by an Illumina 'Next-Seq 500'. My files are in SAM format. My goal is to run Cuff diff and look at differential expression patterns between cases and controls. Our lab already ran a few data cleaning and alignment steps before sending me the clean SAM files. Bowtie 2 was run. I still want to learn how to use Galaxy with these data so I can learn some additional tools beyond what they did with the data already. I am attempting to run tophap and cufflinks in galaxy and got an error for both. I did run the groomer and fastqc and these both worked fine on my files. I used groomer to sort by chromosome and it is now in sanger format ACS II range 35-70. When I ran tophap 2, I got an error that said 'tool execution failed'. It also said 'index error; list index out of range'. I am wondering- do I need to still run this since Bowtie 2 was already ran on my data outside galaxy using the command line? Also are the next-seq 500 files files compatible with galaxy? I tried running cuff link and cuff diff directly without the files and got an error message that says 'cuff link: no update check' and 'cuff diff: command not found'. I appreciate everyone help.
