[BUG] RTS Switching false negative

[Youpu-Chen]

RTS artifacts identification

• I have searched the existing issues

Have you loaded the SQANTI3.env conda environment?

• I have loaded the SQANTI3.env conda environment

Problem description

Hi there. Thank you for this great tool.

I found this could be a false-negative result, therefore directing my question to this bug section.

The yellow and pink alignments down below, were identified as the RTS artifacts.

But the direct repeats were not located near the first red box (left to right). And It was not in line with the representative case of RTS artifacts in PacBio slides.

The direct repeats were found in the second red box.

Could this be a false-negative result?

If you could give me a hint, I'll appreciate it.

Hongpu,
Best regards.

Code sample

I ran SQANTI3 under the 5.3.6 version by default filter.json.

Error

No response

Anything else?

No response

[pabloati]

Hi Hongpu,

Why do you highlight the first square? The detection of and RT switching event is done based on the sequence. SQANTI3 will flag an isoform as having an RT switching event if repetive regions are found in a certain isoform. Those isoforms are flagged because of that reason. However, I cannot tell you much from just that image.

If you want, you could send me the reference genome and annotation and the isoforms, and I will try to replicate the issue :)

Best,
Pablo