identify unmapped regions

Question

[María José]

Hi,

We've created a coverage file of the aligments against the GRCh38 reference genome and we are currently trying to identify regions with zero coverage. We've utilized RepeatMasker and the GAP database from UCSC, but we noticed that there are still many regions that remain unmapped.

I would appreciate any recommendations for additional databases or tools that could assist in identifying these unmapped regions.

Thanks for your help!

[GenoMax]

We've created a coverage file of the aligments against the GRCh38 reference genome

Are you referring to regions that are hard to align reads i.e blacklists as noted in Where to download blacklisted regions?

Additional resource that is recent: https://github.com/dozmorovlab/excluderanges?tab=readme-ov-file

[María José]

We've been analyzing chromosome coverage files for our samples and have encountered some significant gaps with no coverage at all. To investigate further, we downloaded tables from the UCSC Table Browser, as GAP track, RepeatMasker, and blacklisted regions. However, I still find several regions that do not overlap with these coordinates.