Re: [galaxy-user] Cuffcompare .tmap file

Dear all, I have a similar problem when using cufflinks in galaxy (net version). If I didn't select the reference annotation, I can get the FPKM values,but since no reference,I can not get the transcript or gene name. It looks like these: test_id gene_id gene locus sample_1 sample_2 status value_

Re: [galaxy-user] miRNA NGS data processing

Hi Mete, I am not sure it is the "sort" problem. I find "cufflinks" in galaxy is unstable. I have bam files from Tophat which I can run cufflinks a few days agao. But these days when I run cufflinks with these bam files, the error shows. Strangely, it can work some time. I don't know the reason.

[galaxy-user] Any thing wrong with my cufflink process in galaxy?

Dear all: Recently, I run cufflink in galaxy on the internet. I want to compare two samples, However, I found no transcript or gene passed the significant level, even many of them have large FPKM in one sample and 0 FPKM in another sample. Any thoughts? Below is my cufflink process: I have four