search

STOmics / Stereopy

A toolkit of spatial transcriptomic analysis.
MIT License
184 stars 64 forks source link

MIDCount means? #187

Closed predictowner closed 9 months ago

predictowner commented 11 months ago

Hi,

I want to ask a basic question about how the MIDCount was calculated from both GEM and GEF file.

Q1: Based on what I understand, in the GEM file, MIDCount is the fragment counts that dropped on each gene exon region, is that true? Whether alternative splicing forms for same gene are also taken into account? Could I add ExonCount together to get the MIDCount value?

Q2: During switch from GEM to GEF file, is this MIDCount still un-Normalized, which should be the same value in GEM file under same bin condition?

Thanks very much!

UglyRay7 commented 10 months ago

Hi A1: MIDcount is the fragment count dropped on each gene region (exon and intron), which includes ExonCount. In GEM and GEF files you can find ExonCount items directly. A2: It is just a transformation between file formats, not involving changes in values.

Ray