junction_annotation.py bed12 file

[Kokulapalan Wimalanathan]

Hi,

I am currently analyzing some RNA-seq data using RSeqQC and I am interested in identifying the support for known splice junctions for specific genes.

I am currently looking at the BED12 format file "AD_astrocyte.junction.bed". I was wondering how the score was calculated for a particular splice junction.

Is the score just the count of uniquely mapped read? or is it a normalized score?

Thanks,

Kokul

[SCP- 049]

You can consider the score as “number of reads” if one read only split once. But keep in mind long reads can be split twice or more, in this case, one read will be counted multiple times. 

Liguo

On Oct 22, 2022, at 6:28 PM, Kokulapalan Wimalanathan <kokul...@gmail.com> wrote:

Hi,

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