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Old 05-26-2014, 12:40 AM   #1
MaryBioInf
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Default Expand existing transcriptome

I am new to working with NGS data. I want to add the information of new Sequence Reads to an existing transcriptome to possibly identify new transcripts. Does anyone have an idea of how to approach the matter? My first idea is mapping the reads to the trancriptome.
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Old 05-26-2014, 04:59 AM   #2
GenoMax
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That would be one way to identify reads that are mapping to known transcripts.

You can also try to de novo assemble the entire set (or the reads left over after mapping above) using Trinity or Spades (if this is a prokaryotic/small genome).
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Old 05-26-2014, 12:57 PM   #3
Darwin
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Use Tophat and Cufflinks (Trapnell et al. Nature Protocols (2012); http://cufflinks.cbcb.umd.edu/index.html) with the annotation as a guide.

I would not trust it for differential expression of isoforms, but for assembling new transcripts it works fairly well. Only use high quality reads for the assembly and be careful to filter after the final merge.
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