Cufflinks -g vs -G

[budgie lover]

Hi everyone,

I am fairly new to bioinformatics. I was wondering why I would use -g instead of -G in cufflinks. -G is to quantitate against the reference transcript annotation while -g is to use the reference transcript annotation to guide assembly.

Thank you

[manianslab]

Read the manual carefully. -G would not build novel transcripts (novels genes/isoforms) if any found using your RNA Seq reads where as -g would. So depends on what you want.

[mgogol]

Sometimes I run once with -G, once with neither -g or -G (build novel transcripts), then look at novel transcripts that don't overlap with any known genes. I found -g results to be confusing (awhile ago, so maybe it's better now).