reference genome split to chromosomes

[Tereza Jezkova]

I want to map my ddRAD reads to the genome of the axolotl. I downloaded it from GenBank but it comes as separate chromosomes, that is ~20 separate *.fna files. Do I need to merge those into a single *.fasta file? If so, how do I do that? Or is there a way to simply navigate to the folder with the *.fna files and dDocent will somehow figure out what to do?

Thanks, Tereza

[Jon Puritz]

Hi Tereza,

Yes, you should be able to simply concatenate them something like:

cat *.fna > reference.fasta

should work. Though sometimes NCBI makes really ridiculous headers for the sequences. The simpler the better.

Hope that helps,

Jon

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On January 19, 2021 at 3:31:39 PM, Tereza Jezkova (calop...@hotmail.com) wrote:

I want to map my ddRAD reads to the genome of the axolotl. I downloaded it from GenBank but it comes as separate chromosomes, that is ~20 separate *.fna files. Do I need to merge those into a single *.fasta file? If so, how do I do that? Or is there a way to simply navigate to the folder with the *.fna files and dDocent will somehow figure out what to do?

Thanks, Tereza

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