Quick question about Cuffdiff assembly option

Is there any way to forbid transcript assembly and only use the annotation file in cuffdiff/cufflinks? It seems that the software automatically do the assembly even if you feed it with your annotation file.

rna-seq

• 1,475 views • link

updated 9.9 years ago by Jeffin Rockey

• written 9.9 years ago by --panda-- •

1 answer

If you use -G option for cufflinks, the estimation(fpkm tracking files) would be based on the genes and transcripts from the given gtf only.

Similarly in cuffdiff you may provide your GTF in command line prior to the the bam files to have the comparison based on the gtf.

• 0 views • link

written 9.9 years ago by Jeffin Rockey

More posts like this

Cufflinks reports less transcripts then in gff
written 8.6 years ago by grant.hovhannisyan

Hi Biostars, To make transcriptome assembly, I mapped the reads (2x75, strand-specific, organism Candida albicans) with tophat2 and did assembly with cufflinks. The command line …
The right pipline with cufflinks, cuffmerge and cuffdiff
written 9.5 years ago by seta

Hi all, I'm trying to use cufflinks and related programs (cuffmerge and cuffdiff) to find differentially expressed genes and some splicing events between two conditions …
Empty cufdiff output
written 10.0 years ago by Lindsay44 •

I am trying to use Cuffdiff to analyze differential expression between two experimental groups. I used cufflinks and cuffmerge to produce the gtf assembly. When …
Will bowtie multi-valid-alignment-report confuse downstream software?
written 10.0 years ago by --panda-- •

I'm wondering what will happen if we choose the option that makes 'bowtie' report multiple valid alignment to the sam file. Will the downstream software(if …
How to get per sample read counts/FPKM values from cufflinks?
written 10.1 years ago by EpiExplorer

I have couple of questions regarding cufflinks. I have done cufflinks transcripts assembly for 12 cell lines from human.And merged all the transcript.gtf files from …
Upper-quartile normalization option for Cufflinks and Cuffdiff
written 10.2 years ago by trakhtenberg

In the Cufflinks manual (http://cole-trapnell-lab.github.io/cufflinks/cufflinks/#advanced-abundance-estimation-options) it says to use this command: -N/–upper-quartile-norm In the Cuffdiff manual (http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#library-normalization-methods) it says to use this command: --library-norm-method quartile. …
From HISAT2 to cuffdiff?
written 10.4 years ago by dina.hesham139

Hey, I have an issue of not getting any expression values for CDS following: HISAT2 (against hg19) --> cufflinks--> cuffmerge/or cuffcompare--> cuffdiff. Knowing that I …
why does cuffdiff command line contain parameters suited for cufflinks?
written 10.9 years ago by grokaine •

For those who don't know cuffdiff is a program belonging to the cufflinks set of programs designed for RNA-Seq. While cuffdiff is designed to do …
Gene_short_name missing in CuffDiff output (or how to retrieve it?)
written 12.0 years ago by nevev

Dear All, I ran Tuxedo at Galaxy, using TopHat2-Cufflinks-Cuffmerge-Cuffdiff. I expected my Cuffdiff output to contain gene_name, so that I could directly identify genes in …
Cufflinks With Gtf File
written 12.3 years ago by GouthamAtla

Hi, I am working with cufflinks,cuffdiff for RNA-SEQ data. In cufflinks, If we are not looking for novel isoforms, we need to use GTF …