Skip to content
This repository has been archived by the owner on Nov 28, 2020. It is now read-only.

Regions' smoothening

Jump to bottom
Marek Wiewiórka edited this page Aug 31, 2018 · 1 revision

Smoothening of regions:

As a "hole" we call the region that is not expressed. As a "exonlike" we call the region that is expressed.

The main aim of the smoothening is to get rid of very small exonlikes (smaller than 10 nucleotides), that might itroduce some noise in the further analysis. In addition we would like to merge exonlikes that have small holes.

Rules for merging/dividing of regions:

  1. If exonlike is shorter that 10 nucleotides we need to check what is going around it.

    a) If the neighboring exonlikes are distant by at least 10 nucleotides, then such exonlike should become a hole.

  2. If the distance to the next exonlike is smaller that 10 we merge the two exonlikes into one exonlike.

The question is should not we also include the coverage of bams in making rules???

Clone this wiki locally