Hi
I have a question regarding cuffmerge. I thought that the merged.gtf output of cuffmerge contain a new annotation which contains an annotation of known transcripts and also consensus annotation of novel transcripts. I rerun cufflinks for all samples with now use merge.gtf as the reference and I use –G option in cufflinks (result based on only the annotation, i.e., merged.gtf) hoping that cufflink will give results of new annotation (obtained from consensus by cuffmerge) for all samples.
I did it since I need consensus novel transcripts from all samples. Hope any body can help me about it.
Thank you.
I have a question regarding cuffmerge. I thought that the merged.gtf output of cuffmerge contain a new annotation which contains an annotation of known transcripts and also consensus annotation of novel transcripts. I rerun cufflinks for all samples with now use merge.gtf as the reference and I use –G option in cufflinks (result based on only the annotation, i.e., merged.gtf) hoping that cufflink will give results of new annotation (obtained from consensus by cuffmerge) for all samples.
I did it since I need consensus novel transcripts from all samples. Hope any body can help me about it.
Thank you.