Convert .hic and .assembly to pretext?

[sheinasim-USDA]

Hello!

I'm using the Yahs pipeline and creating a sorted scaffold .hic and .assembly file that shows the contig boundaries in Juicebox.

Is it possible to convert my .hic and .assembly file to a pretext file?

I can create a pretext file with the final scaffolds and their contacts, but it doesn't show the contig boundaries.

Best wishes,
Sheina

[conchoecia]

Hi @sheinasim

I'm not a developer for pretextview, but if you have bam files of your reads mapped to the genome then you only need to pipe .sam format into PretextMap to generate a .pretext file to look at in pretextmap. Here's an example.