Hi, by chance can anybody clarify my confusion about cuffdiff.
the input for cufdiff is <transcripts.gtf> and 2 or more sam files. in my case, there are 2 transcripts gtf files (s_7.gtf for widetype and s_8.gtf for treated) and 2 sam files (s_7.sam for widetype and s_8.sam for treated). presumably I should use s_8.gtf for the differentially expressed genes? is this right? it is unclear about the description of transcripts.gtf file in cuflinks manual.
cheers
the input for cufdiff is <transcripts.gtf> and 2 or more sam files. in my case, there are 2 transcripts gtf files (s_7.gtf for widetype and s_8.gtf for treated) and 2 sam files (s_7.sam for widetype and s_8.sam for treated). presumably I should use s_8.gtf for the differentially expressed genes? is this right? it is unclear about the description of transcripts.gtf file in cuflinks manual.
cheers
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