[Gonza]

Hello All,

I am confused with how to match the "XLOC" to the gene annotation. I could see the most diff. expressed XLOC but i do not know the annotation for them (the XLOC is not really useful, i need the annotation).

I run cufflink doing:
$cufflinks -p 8 -o C1_R1_clout C1_R1_thout/accepted_hits.bam

Should i do :
$cufflinks -p 8 -o -G C1_R1_clout C1_R1_thout/accepted_hits.bam

this G is not added in the original protocol but apparently it should be added?
Please let me know!

many thanks

[dpryan]

If you have a reference annotation then you might as well make your life easier and use it. I think you can do this after the fact with cuffmerge, but you'll probably get better results just using the annotation from the get-go.

[Gonza]

thanks, so why does the protocol not say that??? Anyways, i will re-run it with -G now (just to double check with the -G before output):

$cufflinks -p 20 -G genes.gtf -o 02_cufflinks_CTR_R1.Q30.L50.fq 01_tophat2_CTR_R1.Q30.L50.fq/accepted_hits.bam

Thanks again
G

[dpryan]

That paper is just a simple example of how to use the package, it doesn't give details on every possible analysis (that'd be impossible). Odds are that you want -g rather than -G.

[Gonza]

Thanks again, I really appreciate your input.
When I look in cufflinks v2.2.1 -G vs -g this is what it says (below). I am sure what the difference is. Do you still think i should use -g (lower case g). For example:

$cufflinks -p 20 -g genes.gtf -o 02_cufflinks_CTR_R1.Q30.L50.fq 01_tophat2_CTR_R1.Q30.L50.fq/accepted_hits.bam


cufflinks v2.2.1
-----------------
-G/--GTF quantitate against reference transcript annotations
-g/--GTF-guide use reference transcript annotation to guide assembly

[Gonza]

...sorry, i am NOT sure ...

[dpryan]

I'll just mention that if you use -G then there's no point in using cufflinks at all (this probably just becomes a slower version of cuffquant or rsem with -G). Much of the point of cufflinks is to find either new features in your genome or modify existing ones to better match your dataset. With the -G option, you're telling cufflinks to not do any of that. That's fine, but cufflinks is slow, so there are much faster ways of going about getting that information. So, you want -g.

[Gonza]

ok, thanks very much for the information
G