RABT by cufflinks

Question

[EpiExplorer]

Hi,

I realised that while running cufflinks I missed an option of -g GTF-guide and I ran cufflinks with only --GTF option. What would be the difference in results of cufflinks assembly without using -g option? I wanted to do reference guided assembly.

Here is my command: cufflinks -p 8 -o /home/cufflinks --library-type fr-firststrand --GTF Genes/genes.gtf Sample1_Merged.bam

Thanks.

Answer 1

[EpiExplorer]

I think I figured out the difference. The confusion was because I thought -G and -g needs to be applied together. But actually for reference guided assembly, only -g option is required. The command that I ran before would only assemble known annotations through GTF file.

Sorry for creating a new post for this silly question.

[Ram]

No worries, it's OK :)