Improve accuracy of trinity RNA-Seq assemblies with --min_glue and/or --min_kmer_cov

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gwilymh

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Join Date: Dec 2011

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Improve accuracy of trinity RNA-Seq assemblies with --min_glue and/or --min_kmer_cov

11-26-2014, 05:37 PM

Hi,
Does anyone know if it possible to improve the accuracy of Trinity RNA-Seq assemblies using --min_glue and/or --min_kmer_cov flags?

The trinity manual suggests raising the --min_kmer_cov value from the default (1) to 2 to save on memory usage and eliminate rare, inaccurate reads. Would it be advisable to raise this to higher, maybe to 4 or even to 20?

Similarly, has anyone tried raising the --min_glue to, say, 10 to improve the accuracy of the assembly?
Tags: accuracy, rna-seq, rna-seq aligners, trinity assembly

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