Question: Cuffcompare on the merged GTF file produced by Stringtie
gravatar for seta
3.0 years ago by
seta1.2k wrote:

Hi all,

For doing an RNA-seq analysis, I used STAR for mapping reads to the genome followed by Stringtie for genome-guided assembly. I downloaded the GTF file of my organism (a plant) and merged it with the annotation file produced by Stringtie for Cuffdiff analysis. (I don't want to use ballgown package). I used cuffdiff from cufflinks-2.2.1 package for differential expression analysis. But among the cuffdiff outputs, just gene_exp.diff and isoform_exp.diff are filled with results and splicing.diff, promoters.diff and cds_exp.diff are empty. As I searched, I found the below command to obtain the combined.gtf file that contains tss_id and p_id, required for getting splicing.diff and promoter.diff results from cuffdiff analysis.

cuffcompare -s /path/to/genome_seqs.fa -CG -r annotation.gtf annotation.gtf

I was wondering if I can use the merged GTF file produced by Stringtie along with original GTF file in the above command?


ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 3.0 years ago by seta1.2k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 774 users visited in the last hour