Edit in Exon vs Edit in CDS

[jtls0n]

I was confused by some of the Edit df output where some sgRNAs are listed as TRUE for Edit_in_CDS, but FALSE for Edit_in_Exon

I can understand the opposite (in Exon but not coding), but in CDS and not in Exon is confusing.

Is this just an annotation difference between Exon and Transcript? Or, is there something else I am missing.

Thank you!

[CansuDincer]

Many thanks for reaching out!

These regional annotations are retrieved directly from the Ensembl API. If you can send the gene of interest and the run options, I can look into it in more detail.

[jtls0n]

Thanks for following up! There is the command I used to run.

 python3 BEstimate.py \
 -gene RUNX3 \
 -assembly GRCh38 \
 -pamseq NGG \
 -pamwin 21-23 \
 -actwin 4-8 \
 -vep \
 -protolen 20 \
 -edit C \
 -edit_to T \
 -o ../output/ \
 -ofile RUNX3_CBE_NGG