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Old 01-03-2012, 02:42 PM   #1
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Location: Townsville, Australia

Join Date: Dec 2011
Posts: 6
Default Aligning transcritptome with trimmed or untrimmed data

I recently aligned the transcriptomes of 5 different algal species, using oases.

I found that I get higher N50 values and maximal contig lengths if I use the untrimmed data. Furthermore, even though the percentage of reads used is higher if I use trimmed data, overall with the massive reduction in data if I trim it, I use more of my reads if I assemble the transcriptomes with untrimmed data.

I know one side effect of sequencing errors is a higher RAM requirement, but besides that, is there any other negative (or positive) effect if I use untrimmed data for my assembly?

RAM wasn't really an issue for me, since I had access to a high performance computer with several nodes with 64 GB RAM each.
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