Re: question on mappability gaps in mm10

[Mehran Karimzadeh]

Hi James,

Gaps in the bed files mean that the region is not uniquely mappable with k-mers of length 24.

Mehran

On Mon, Jun 24, 2024 at 11:35 AM James Dalgleish <jame...@gmail.com> wrote:

Sorry if this is an obvious question, but how would I get mappability for the bases between 3000042 and 3000124 for mm10? I need to get mappability values to the smallest possible window I can.

```

/code/shell/mappability/umap/mm10$ zcat k24.umap.bed.gz | head
track name="<type 'type'> 24"description="Single-read mappability with 24-merscolor=%s
chr1 3000001 3000042 k24 1 +
chr1 3000124 3000148 k24 1 +

```

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