How to use cufflinks only to assemble transcripts, but not estimate abundance?

[manianslab]

We use the tophat-cufflinks-cuffmerge-cuffdiff pipeline for RNA Seq analysis. I am wondering if there is a way to have "cufflinks" - the command not the package - just do the transcript assembly since we never use the fpkm outputs from it anyway?

[cedance]

Just run Cufflinks alone. Cufflinks provides a transcript.gtf file which consists of all possible transcripts. You could use gffread then and provide your reference genome and this gtf to obtain a transcript fasta file. For your case, you just wouldn't continue with any of the other modules they have for downstream analysis. Is this what you were asking for?

[manianslab]

@cedance: Thanks for your response. My post perhaps was not clear. After the cufflinks run, we use cuffmerge to generate merged gtf and then run cuffdiff on it on each of our bam files. But, I see that cufflinks also spends time doing abundance estimates using the GTF file provided for guidance assembly (RABT) - I dont think these abundance results are used by any downstream application. I was wondering if there was a way to avoid this.