Galaxy Cufflinks -> cummeRbund?

[hyates]

Hi,

I found a useful thread here that is related to what I am doing, but not quite. Galaxy may be missing some files I need? I don't know. Here is what I want to do.

1. Read in cuffSet object using readCufflinks()
cuffData = readCufflinks("data")

2. Once I have this cuffData, I want to draw a volcano plot as follows
sigGene = csVolcano(genes(cuffData), "treatment1", "treatment2")

That's it.

My problems are as follows:
1. See my attached files. I need to save galaxy output to be recognized by readCufflinks(). However, see my error message. I am going to need all the default files readCufflinks requires. But I don't see where galaxy saved isoforms.fpkm_tracking. I just don't see it? Is it transcript FPKM tracking?

2. If all I want is to make a volcano plot as mentioned in 2. Can I just load the gene diff and fpkm tracking file for readCufflinks? Or do I need all the output from galaxy?

3. Right now I am manually saving the output files and renaming them, but is there a better way to output galaxy cufflink output?

[hyates]

I think I may have found the solution here. However, before I can claim this is solved, can I have some folks in the community confirm some things for me? For example, that transcript differention expression from galaxy output is actually isoform.diff and so on? Why would they name files different like this from cuffdiff output defaults? I am just trying to figure out what is galaxy calling an output and what cummeRbund thinks it is. I am, I think, super close.