Question: Transcriptome assembly with Cufflinks
0
gravatar for tawares07
2.9 years ago by
tawares070
Brazil
tawares070 wrote:

Hi Biostars community,

I did a transcriptome assembly using Cufflinks with a bam file aligned by Novoalign.
Run: ERR030887.
Parameter: -g (Tells Cufflinks to use the supplied reference annotation a GFF file to guide RABT assembly.)

However, I really don't know how to select the best assembled transcripts. So, here are my questions:

1) What are the decisive criteria to select the best assembled transcripts based on Cufflinks output?
2) Is it possible to know or identify exactly the reads used to assembly the transcripts?

Thanks for your attention,
Raphael Tavares

ADD COMMENTlink modified 2.9 years ago by Jennifer Hillman Jackson23k • written 2.9 years ago by tawares070
1
gravatar for Jennifer Hillman Jackson
2.9 years ago by
United States
Jennifer Hillman Jackson23k wrote:

Hello,

The manual for Cufflinks is here:
http://cole-trapnell-lab.github.io/cufflinks/cufflinks/index.html

To answer what the best transcripts are can depend on what you are interested in. See the output files - you could for example only choose transcripts that were represented (had complete coverage) by your read data.

To my knowledge, Cufflinks does not report where each individual short read was mapped to transcripts (this is assumed to be one-to-many by design).

Thanks, Jen, Galaxy team

ADD COMMENTlink modified 2.9 years ago • written 2.9 years ago by Jennifer Hillman Jackson23k

Your are right, Jennifer.  Cufflinks does not report where each individual short read was mapped to transcripts.

Someone suggested me to align all reads using only the sequences from the transcripts of the gft file. So, I will have an idea of which reads were "used" in the assembly. But I don't think this is the correct way to identify the reads that I want. 

Thanks again!

ADD REPLYlink written 2.9 years ago by tawares070
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