Question: Re: Cufflinks Merging More Than One Transcript On Bacterial Genomes
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Jeremy Goecks • 2.2k wrote:
Noa,
I'm not sure that folks on this list have much experience with
bacterial transcriptome analysis. You might try seqanswers.com or try
emailing the Tophat/Cufflinks authors directly:
tophat.cufflinks@gmail.com If you find something interesting in
another place, please feel free to share with the Galaxy community.
Reference genome or reference gene annotation? Using a genome to
correct for bias should not change the assembled transcripts, only
their expression levels. You can use a reference gene annotation
either as ground truth or as a guide; using the reference as ground
truth ensures that Cufflinks will only assemble transcripts defined in
the annotation.
Good luck,
J.