can suppa2 do the analysis of microorganisms?

[cent0134]

Hello developers,I would like to ask the following, can suppa2 do the analysis of microorganisms, such as viruses?

[EduEyras]

Hi, Yes, if you have an annotation or can build one. If you don't have an transcriptome annotation readily available, you can build one from the RNA-seq using StringTie2, FLAIR, Bambu, etc.. depending on whether you have short or long reads, or both. You can then quantify the transcriptome and apply SUPPA as usual. You can use the variable boundary option "-b V" to provide additional flexibility in the definition of alternative splicing events, in case this is relevant in your micro-organism. I hope this helps Eduardo

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