Autosome/ sex chromosome assembly error

Question

[Megan]

Hi,

I'm doing a coverage analysis to identify the W chromosome in a chromosome level genome assembly from a female snake, (the genome on NCBI does not have chromosome names assigned to scaffolds). I found that there was an assembly error in the reference genome, and a chunk of an autosome scaffold is attached to the W scaffold. My question is, what tools can I use to separate out the W from this scaffold and create a new scaffold with just the W? Thanks!

[samuel.a.odonnell]

If you know what the chunk is (I guess you could try define the edges by alignment to autosomes etc), can you not just remove it manually? Are you also sure that it is incorrect and that you are just not looking at some variation?