Transcriptome assembly with Cufflinks

[Tavareseq]

Hi NGS 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,
Tavareseq

[TiborNagy]

For your second question: you need to map the reads back to the reference.