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Old 01-22-2015, 09:54 AM   #1
Junior Member
Location: Brazil

Join Date: Nov 2014
Posts: 1
Smile Transcriptome assembly with Cufflinks

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,

Last edited by Tavareseq; 01-27-2015 at 06:27 AM.
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Old 01-23-2015, 04:40 AM   #2
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Location: Budapest

Join Date: Mar 2010
Posts: 329

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