Tweet
Hi community!
I'm working with a dolphin species, Tursiops truncatus reference genome on a RADseq approach, and my analysis requires the absence of the sex chromosomes.
Looking into my VCF file, the chromosome names start with NW_ instead of NC_ (NCs table available: https://www.ncbi.nlm.nih.gov/genome/?term=txid9739[orgn]).
Those NWs are, apparently, scaffolds prior to assembly into chromosomes.
So, I've been trying to find the "translation" between these NWs and the NCs, but nothing until now.
The reference is from a female so, I need to find a way to identify the X chromosome and discard it.
An option would be to redo everything from the alignment stage but using a new reference genome that doesn't include the X chromosome.
Previously I downloaded the genome in the fasta format also from that page. But how could I discard a chromosome from the entire file?
I was wondering if you could help me with this.
Thank you in advance
All the best!
I'm working with a dolphin species, Tursiops truncatus reference genome on a RADseq approach, and my analysis requires the absence of the sex chromosomes.
Looking into my VCF file, the chromosome names start with NW_ instead of NC_ (NCs table available: https://www.ncbi.nlm.nih.gov/genome/?term=txid9739[orgn]).
Those NWs are, apparently, scaffolds prior to assembly into chromosomes.
So, I've been trying to find the "translation" between these NWs and the NCs, but nothing until now.
The reference is from a female so, I need to find a way to identify the X chromosome and discard it.
An option would be to redo everything from the alignment stage but using a new reference genome that doesn't include the X chromosome.
Previously I downloaded the genome in the fasta format also from that page. But how could I discard a chromosome from the entire file?
I was wondering if you could help me with this.
Thank you in advance
All the best!