I have sequenced the rhodopsin gene of philautus in Illumina genome analyzer which gives paired end reads. I obtained 10 contigs from the paired reads using Velvet 1.1.10 and then scaffolded the contigs using SSPACE. However the output was 10 scaffolds which are essentially the contigs just rearranged. How can I use these scaffolds to reconstruct the gene in the forward sense? The order of the scaffolds is not the actual order of the gene.
PS: I do not have a reference genome, only 2 reference exons of the gene.
I have not much experience in Eukaryotic gene sequencing, but here it kind of seems you amplified only that specific gene from your philautus specimens DNA using PCR and then constructed an Illumina library from that?
So wouldn't Sanger sequencing/primer walking of the product be an alternative (or at least now help to connect those Illumina contigs)?
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