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Old 02-08-2011, 06:30 PM   #1
blindtiger454
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Location: Omaha, NE

Join Date: Oct 2010
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Default Removing contaminants, transposons, dark matter before mapping

We are working with a novel plant transcriptome (no reference genome). After annotating the assembly, will removing irrelevant contigs effect read mapping statistics, in a good way, when we perform RNA-Seq analysis? Many of our contigs annotate as retrotransposons, bacterial/viral contaminants (metagenomic leftovers), or have no match to any annotated proteins in public databases. I assume contaminants should be removed, but what about genes of no interest to our research (e.g. transposable elements)? Will our results be more accurate if the our transcriptome only contains known and relevant protein coding contigs?
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