hi all,
I am using the cufflinks->cuffmerge->cuffdiff pipeline to assemble transcripts (known and novel) and perform differential analysis. I am not sure if I should use the parameter -g to "guide" the assembly using an annotation.
I am not sure how much difference using or not this parameter if I want to identify novel transcripts. Maybe this parameter should not be used in thecufflinks step but in the cuffmerge step instead.
Any advice will be appreciated.
I am using the cufflinks->cuffmerge->cuffdiff pipeline to assemble transcripts (known and novel) and perform differential analysis. I am not sure if I should use the parameter -g to "guide" the assembly using an annotation.
I am not sure how much difference using or not this parameter if I want to identify novel transcripts. Maybe this parameter should not be used in thecufflinks step but in the cuffmerge step instead.
Any advice will be appreciated.
Comment