How to explain the result of class code in cuffcompare?

Hi,everyone,

I am using cuffcompare now, if a cufflinks transcript shares = or c class code with reference transcript, can I say this cufflinks transcript is a known transcript and the transcripts with other class code can be seen the novel transcripts.

Thanks very much if someone give me some advice.

cufflinks rna-seq cuffcompare

• 2,875 views • link

updated 3.7 years ago by Ram

• written 11.1 years ago by zm20074970 •

0 answers

No answers yet.

More posts like this

the reference used in Cuffcompare(GENCODE, RefSeq)
written 2.0 years ago by ZZOYEA •

Hello. I am currently conducting RNA-seq analysis and trying to identify novel transcripts using Cuffcompare by comparing with a reference. I performed Cuffcompare using GENCODE …
error in compare.py of CNCI package
written 8.0 years ago by priteshrhsabara •

Hi, I am currently working on lncRNA using CNCI package. I have identified more than 10,000 coordinates of probable lncRNA using cufflinks-cuffcompare, based on class-codes …
Transcript to gene mapping of overlapping transcripts from cuffcompare
written 9.2 years ago by sunil.mangalam •

Hi Forum, We did RABT assembly of mouse transcriptome using cufflinks and stringtie. Cuffcompare produced many genes of the class code O. While mapping these …
Cuffcompare. Differences between class codes "=" and "i"
written 10.8 years ago by Antonio R. Franco

According <a href="http://cole-trapnell-lab.github.io/cufflinks/cuffcompare/">THIS DOCUMENT</a>, after nunning cufflinks/cuffcompare to reconstruct the transcripts with a gtf reference genome Class code "=" is a Complete match of intron …
How to use Rfam annotate small RNA and how to see differential expression of novel miRNA produced b…
written 11.2 years ago by zm20074970 •

Hello everyone I am analyzing small RNA data currently, but there are some questions about Rfam and mirdeep result? could someone give me some advice, …
Help with identifying novel transcripts
written 11.5 years ago by martyflores •

I am trying to identify novel transcripts across two developmental stages. We'll call them dev1 and dev2. I have the RNA-seq for dev1 and dev2 …
Cuffcompare with a single experiment and questions regarding cuffcompare output
written 12.2 years ago by jacobsen.jeremy •

I am running RNA-seq analysis on a paired-end deep sequencing data set with no replicates. We are interested in finding novel gene and transcript isoforms …
Inferring Novel Exons From Rna-Seq Data
written 13.5 years ago by toshnam

Hi, I wonder if I can infer novel exons in RNA-Seq. I'm used to use TopHat and Cufflinks for read alignment and …
Validate Novel Isoforms Generated By Cuffcompare
written 13.8 years ago by Ge •

When I compare the assembled transcripts with a reference annotation with cuffcompare, one of the output files is cuff_in.tmap. According to class code column in …
Cuffcompare Class Code "U" Transcripts
written 13.8 years ago by upendrakumar.devisetty

I thought cuffcompare class code "u" transcripts are novel. But when i blasted those class code "u" transcripts against reference annotated transcriptome i found ~20% …