search

lemene / PECAT

PECAT, a phased error correct and assembly tool
BSD 2-Clause "Simplified" License
41 stars 1 forks source link

Sex Chromosome Phasing? #40

Open Brooklynvcx opened 4 days ago

Brooklynvcx commented 4 days ago

Hello! In your paper you mentioned that sex both chromosomes are placed in haplotype 1, "PECAT places the contigs of X and Y chromosomes in the primary contigs or the haplotype 1".

I was wondering if that is the case for an XX sample and XY, or would an XX sample phase in both haplotypes and the variants for the genes on the X chromosome is placed in alternate similar to the other chromosomes?

In the event X or Y chromosomes are placed in primary and haplotype 1, how do you determine which ones are the sex chromosomes?

I specifically need to phase the X chromosome, so any additional information you had regarding PECAT's X and Y chromosome phasing would be great appreciated!!!

Here are the number of contigs after polishing for reference: Primary: 2748 Alternate: 3431 Haplotype 1: 2656 Haplotype 2: 1608 Rest: 57

Thank you

lemene commented 4 days ago

Hi, @Brooklynvcx In PECET, both X and Y are located in primary.fasta or haplotype_1.fasta, while X and X are found in primary.fasta/haplotype.fasta and alternate.fasta/haplotype_2.fasta, similar to other chromosomes. The main reason is that it is difficult to find the correspondence between X and Y. To determine whether contigs are from X or Y, it is necessary to align them to a reference genome. Without a reference genome, PECAT cannot distinguish which contigs belong to X and which belong to Y.