Hello, I tried to use Cufflinks after hisat2 but I only have genes with names as CUFF1 etc. and chromosome locations. Finally I downloaded GTF file from Cufflinks website but still I have many genes with CUFF name and without gene name. What can be the main reason of this? Genes with unknown names?
Thank you.
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written
by
hkarakurt
1 answer
cufflinks -h :
-L/--label assembled transcripts have this ID prefix [ default: CUFF ]
If you run cufflinks without a GFF/GTF file, it will assemble transcripts on its own and give them the prefix "CUFF". If you provide a GFF/GTF, it will quantify the genes/transcripts that you provide there, plus assembling them on its own as well where not present.
If you add -G:
-G/--GTF quantitate against reference transcript annotations
It will quantitate only the ones specified in the GFF/GTF.
If you use the -g instead, it will make its own transcript assembly but using your own GTF as guide.
-g/--GTF-guide use reference transcript annotation to guide assembly
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