TEannot Output

[KHANYAP4]

Hey Jeremy, thank you for constructing PiRATE, this is such a wonderful tool and it's easy to work with. I have done all the detection steps and classification successfully even the annotation step with TEannot. Now I have see that you recommend a second run in the TEannot step using the TE sequences in the Full Length copy file as input in the second run. So now my question is based on the proportion of each TE class. Do we use the outputs of the second run to calculate TE content. Based on my results, I only have 4 sequences in the Fully Length copy file and I have used that in the second run, and received the GFF3 file, Full length copy file etc.

Best regards Khanya

[JBerthelier]

Dear Khanyap4,

Thank you for your message,

Yes you have to use the gff3 file obtained with the second run of TEannot. However, I am a bit surprised that you found only 4 sequences in the FLC output. What tools did you used for the TE detection ?

Best regards

Jeremy