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Dear All,
I get reads specifically for the target genes in different species. There is a genome which is close related to the species I am interested in will be used as a reference genome.
The question I am confusing about is that how to avoid big gap between your species and the reference genome.
For example, if the gene in my species have a big insertion (like 4kb), then the reads from this region will not map onto the reference genome, because the reference genome do not have this region. So to avoid this, 1. I used Software Geneious to do de novo assemble first, then I got several hundred contigs (I don,t know why I get so many contigs! because ideally the reads I got should be specifically for the gene I am interested in). 2. I mapped all original reads to the reference genome to get consensus sequence. 3. I map both the contigs from step1 and the consensus sequence from step 2 to the reference genome again, to see whether contigs from de novo assemble can detect big gap between my species and the reference genome.
Is this method OK? I am not sure that if the contigs from de novo assemble which include big gap region (like I mentioned above, 4kb insertion in my species) can map onto the reference genome (which do not have this 4kb insertion)?
Looking forward to your suggestion.
Best,
Sadiexiaoyu
I get reads specifically for the target genes in different species. There is a genome which is close related to the species I am interested in will be used as a reference genome.
The question I am confusing about is that how to avoid big gap between your species and the reference genome.
For example, if the gene in my species have a big insertion (like 4kb), then the reads from this region will not map onto the reference genome, because the reference genome do not have this region. So to avoid this, 1. I used Software Geneious to do de novo assemble first, then I got several hundred contigs (I don,t know why I get so many contigs! because ideally the reads I got should be specifically for the gene I am interested in). 2. I mapped all original reads to the reference genome to get consensus sequence. 3. I map both the contigs from step1 and the consensus sequence from step 2 to the reference genome again, to see whether contigs from de novo assemble can detect big gap between my species and the reference genome.
Is this method OK? I am not sure that if the contigs from de novo assemble which include big gap region (like I mentioned above, 4kb insertion in my species) can map onto the reference genome (which do not have this 4kb insertion)?
Looking forward to your suggestion.
Best,
Sadiexiaoyu