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?
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?
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