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Minimum amount of reads for de novo plant transcriptome assembly mruizm Bioinformatics 3 09-09-2013 02:54 AM
Minimum coverage needed of de novo small RNA sequencing hechanner Illumina/Solexa 0 02-22-2012 06:09 PM

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Old 08-25-2013, 10:18 PM   #1
Location: Santiago

Join Date: Apr 2013
Posts: 22
Default Minimum deep of coverage in a de novo transcriptome analysis

Hi everyone, i have 4,46 Gigas of information on various sequencing of transcripts in various tissues of Illumina Miseq paired-end reads. I had assembly all these reads and i found that the mean deep of coverage is of 27,9X (Deep of coverage = efficiency of sequencing / efficiency of assembly)
My question here is, what is de minimun of the deep of coverage for obtain robust information of the assembled transcriptome in a de novo transcriptome analysis?

Best regards!
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Old 09-09-2013, 02:50 AM   #2
Location: Cambridge, UK

Join Date: Dec 2011
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28X coverage is plenty for assembly of most transcriptomes - I usually digitally normalise coverage down to 20X using khmer.

Of course it's the extremes that matter - 28X coverage likely means just a few genes account for the majority of the reads, and a large number of reads will have very low or no coverage. If your aim is to quantify the most abundant genes, no problem. If you have some other goal, you may want to consider what your coverage distribution means for your goal.
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