Cufflinks gives only CUFF names with a gtf.

Question

[hkarakurt]

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.

Answer 1

[Matteo Schiavinato]

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