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Old 02-10-2012, 11:13 AM   #2
ssing
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Location: usa

Join Date: Jan 2009
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Hi LizBent,

I have been working on the exact same problem and have come up with some metrics to estimate the quality of a transcriptome in the absence of a ref genome. Some stats that I have used are:
*n50
*percent annotated to my closest reference
*percent of annotated proteins that have (what seem to be) premature stop codons
*percent of reads used/percent of paired reads used
*contiguity & completeness (see http://www.nature.com/nrg/journal/v1...l/nrg3068.html)
*incidence of chimeric transcripts

As for calculating simple metrics like n50, max contig size, etc, I use the command line program abyss-fac, which is available as part of the general ABySS package.

Good luck!
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