Interpretation of outputs

[yanwang271]

Hi,

Thanks for the nice tool.
I ran it with --raw_score True, and saw scores for each tissue. Are these scores tissue-specific delta scores, which can be selected as splice-disrupting when > 0.27 ? Or, these scores have different meaning?

Regards,
Yan

[SilverNebula]

Hello,

The scores generated using the --raw_score option represent the initial delta scores, which have not yet been transformed into tissue-specific delta scores. These are similar to the "delta Brain" values mentioned in the "Method - Quantifying splicing change resulting from variants" section of our manuscript.

(For detailed code, please refer to:

SpliceTransformer/sptransformer.py

Line 116 in b67a51d

if output_raw:

)

Additionally, the threshold of 0.27 applies specifically to the ΔSplice score, as displayed in the 'score' column of the output file. This threshold remains consistent regardless of the --raw_score setting. If the 'score' is below 0.27, it suggests that the SNV is unlikely to significantly disrupt splicing, and consequently, the tissue-specific scores may not be meaningful in this context.

Best regards,
ShenLab