Assess Cufflinks assembly

Question

[int11ap1]

Hello everybody,

I have carried out an RNA-seq project in order to identify putative novel isoforms and genes in different plant annotations with TopHat/Cufflinks. Is there a way to assess the quality of my new annotations compared to the reference annotations?

Thank you.

[Martombo]

if I understood correctly, you're looking for new isoforms and genes in a species in which there's already an annotation available, right?. I guess you could try to do a de-novo assembly (ignoring the annotation) and see how this compares with the first one you did. how many transcripts are found again and how many counts are assigned to each of them.

[int11ap1]

I already have discovered new isoforms. I just want to assess which annotation is better (mine or the reference one) according to the FASTQ file or reads I used.

Answer 1

[sayuj.koyyappurath]

Hi

Please see the old posts in Biostar itself, may be you have seen it already!

• Assessing The Quality Of De Novo Assembled Data
• Assessing Quality And Accuracy Of De Novo Genome Assembly

Best wishes

Sayuj

[Martombo]

these posts are about genome assemblies, while the question was about a transcriptome assembly