Map genome to a particular region

Question

[JohnOak]

Hi everyone,

This is probably a stupid/easy question but I'm feeling a bit lost and any help would be much appreciated.

I extracted a particular genomic region of interest (centered around a gene) from a chromosome-level genomic assembly. I have a reference genome (not as complete) from a closely related species. I would just like to map the data that I have from this closely related species to that particular genomic region of interest.

Should I just use bwa-mem with the sequence of the region of interest as the reference or will this cause undue problems?

Thanks in advance!

[GenoMax]

If you are using the selected region as a query against a different genome then it should not cause any issues. Do you have sequence data or just a sequence (what length) that you have extracted. If you have latter using bwm mem would likely not be appropriate.

[JohnOak]

So, you're saying that using the region of interest as a query in BLAST (for instance) should be okay? For the region of interest, I have a FASTA file with 10kb either side of the gene.

[GenoMax]

Yes it should be fine to use BLAST. If it will work well or not will depend on how closely related the second genome is and the quality of sequence available.

[GenoMax]

You could also try to use a long read aligner like minimap2 is the genomes are reasonably close.

Answer 1

[Pierre Lindenbaum]

e or will this cause undue problems?

this will cause problems see: Exome Sequencing: Masking The Non-Genic Sequences ?

[JohnOak]

Thanks! Do you have any recommendations about the best way to do this then? Even if you can provide just a brief overview of the required steps, that would already be quite helpful.