BS junction sequences: one-base shift

[YunaBlum]

Hi David,
Thank you for the updated code for the BS junction sequence. I still have a minor pb when using Ciri output as it uses bwa and not STAR there is a shift of one base that appears in the sequence. For instance, when using the default data resulting from Circexplorer, your tool gives this BS sequence for HIPK3:

Using CIRI output only, for the same circRNA your tool gives:

Best,
Yuna

[davhum]

Hi Yuna,

Thanks for identifying this issue. I have amended this so that the correct output is generated for CIRI data.

This issue has reminded me that the BSJ sequence retrieved is obtained from the genome without any cross reference to gene model. The current implementation extends 125nt both directions from the BSJ. In some cases this length will extend beyond the exon boundary. I should properly define/document this so will leave this issue open and update vignette and Ularcirc page accordingly.

Regards,
David

[YunaBlum]

ok thank you