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.
1 answer
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.
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