Hi, sorry to bug with probably a naive question. I'm new to cufflinks. I am exploring all the tools. I have two main issues:
(1) I tried all the possible reference annotation files (refseq, UCSC, ensemble) but the output file of cufflinks (.gtf) doesn't have the gene_name even if for example the ensemble GTF files has it. SO my question is: how can I keep this info? Is it like that because you upload the file in UCSC without looking at it like a text file?
(2) If I have different samples (lets say brains of different people) and I want to evaluate the DE among them do I have to us ethe cuffmerge or the cuffcompare script?
-for testing I have one control brain and one affected brain: after having run cufflinks I have two transcipt.gtf. Do I have to use cuffcompare (to get a unique .gtf) and then cuffdiff?
-I will have four control brain and four affected brain, do I will have 8 transcripts.gtf files. Do I have to use cuffmerge grouping the 4 controls (producing one control.gtf file), the same for the cases (producing a cases.gtf). And then I have to use cuffcompare between the control.gtf and cases.gtf file having a unique .gtf file and then cuffdiff?
I don't understand if cuffmerge is to merge together ssample of the SAME groups and cuffcoimpare to unify different categories of samples..
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