I every one, is my first time here but I follow for many months. My question is if someone have experience with genome assembly and post mapping of ran-seq data.
I use velvet, celera and clc to make de novo assembly of relative difficult bacteria, and i have relative goods statistics with velvet and celera (revised with published draft genomes). Then I check the assemblies mapping rna-seq data of the same organism and I obtain lows mapping percentages (near 50%) but when I check clc assembly this up to 90%. I try to optimise the clc assembly but if I drecrease the data or make more stringent trimming, the assembly decrease in quality.
I use 250pb PE in miseq plataform.
Best regards !
Cristian.
I use velvet, celera and clc to make de novo assembly of relative difficult bacteria, and i have relative goods statistics with velvet and celera (revised with published draft genomes). Then I check the assemblies mapping rna-seq data of the same organism and I obtain lows mapping percentages (near 50%) but when I check clc assembly this up to 90%. I try to optimise the clc assembly but if I drecrease the data or make more stringent trimming, the assembly decrease in quality.
I use 250pb PE in miseq plataform.
Best regards !
Cristian.
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