Run SQANTI3 with annotated reference Genome but no annotated reference Transcriptome?

[KeSchus]

I will do a comparison of alternatively spliced genes between 2 states and already have an annotated reference genome but no annotated reference Transcriptome. Is there a way to get around that in the QC step?
Could I take the transcriptome of 1 state as a reference Transcriptome for the other state and vice versa?
Thank you in advance.

[TianYuan-Liu]

Hi KeSchus,

To better assist you, could you please specify which species you are using for your analysis?

Additionally, one approach to address the lack of a reference annotation is to use the Liftoff tool. Liftoff can help you map annotations from a closely related species' reference genome to your species of interest. You can find more details about Liftoff in this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8289374/.

As for your question, using the transcriptome of one state as a reference for the other and vice versa could introduce bias and complicate your analysis. It’s generally more reliable to use a properly annotated reference if possible.

Tian

[KeSchus]

Hi Tian, thank you for your quick response and input. I am comparing differential Splicing between the symbiotic and aposymbiotic states in the anemone Aiptaisia using Oxford Nanopore longreads. I'm still a little confused. I do have an annotated genome and my own Transcriptome as well (I did 3 assemblies using different tools). But there is no accessible annotated reference Transcriptome. I thought I just might take raw sequencing data from NCBI and do it myself just so I have something as input for the QC step. I proceeded using SUPPA2 first but am planning to still do the SQANTI analysis afterwards and compare the outcomes. And yea your point with introducing a bias makes sense, so I'll just have to figure out a way around that. Thank you! cheers, Kevin Am Mittwoch, Juni 05, 2024 17:23 CEST, schrieb Tianyuan Liu ***@***.***>:

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Hi KeSchus, To better assist you, could you please specify which species you are using for your analysis? Additionally, one approach to address the lack of a reference annotation is to use the Liftoff tool. Liftoff can help you map annotations from a closely related species' reference genome to your species of interest. You can find more details about Liftoff in this article: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8289374/. As for your question, using the transcriptome of one state as a reference for the other and vice versa could introduce bias and complicate your analysis. It’s generally more reliable to use a properly annotated reference if possible. Tian -- Reply to this email directly or view it on GitHub: #305 (comment) You are receiving this because you authored the thread. Message ID: ***@***.***>