Hello,
I have two different strains of the same bacteria, strain A and strain B. I assembled both of these using trinity de novo, and I also have a reference genome for each strain, with reads aligned using bowtie. I want to find a way to make a mapping/clustering between strain A's de novo assembly, and strain B's de novo assembly. I also want to be able to make the same kind of mapping between strain A's de novo, and strain A's reference genome.
What I have:
What I want:
What I need:
So how can I get that mapping? I realize it wont be a 1-to-1 mapping, but with closely related sequences like this I could at least identify a majority of genes. If it's not something commonly done, can someone at least point me in a promising direction? Thanks very much for any suggestions you can offer.
I have two different strains of the same bacteria, strain A and strain B. I assembled both of these using trinity de novo, and I also have a reference genome for each strain, with reads aligned using bowtie. I want to find a way to make a mapping/clustering between strain A's de novo assembly, and strain B's de novo assembly. I also want to be able to make the same kind of mapping between strain A's de novo, and strain A's reference genome.
What I have:
- strain A: trinity de novo assemble (fasta)
- strain B: trinity de novo assemble (fasta)
- strain A: reads mapped to de novo assembly (bam)
- strain B: reads mapped to de novo assembly (bam)
- Strain A: reads mapped to reference genome via bowtie2 (bam)
- Strain B: reads mapped to reference genome via bowtie2 (bam)
What I want:
- Compare gene expression levels across assembly methods.
- Compare gene expression levels for same assembly methods, across different strains.
What I need:
- A method to identify which genes are which between these data!
So how can I get that mapping? I realize it wont be a 1-to-1 mapping, but with closely related sequences like this I could at least identify a majority of genes. If it's not something commonly done, can someone at least point me in a promising direction? Thanks very much for any suggestions you can offer.
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