add_transcripts

[zpliu1126]

Hi @diegozea :
As you mentioned in document. same question as me #4

This script add_transcripts should run after transcript_query and before thoraxe.

If the species I am studying is not a model species, I cannot use transcript_query to query. How should I organize the input files required by thoraxe ?

Best wish
zpliu

[diegozea]

Dear @zpliu1126,

Thank you so much for your question about using our software for species not represented in the Ensembl database. I appreciate your interest and would be happy to help you in any way. Here is the suggested workflow:

1. Run transcript_query with the model species: Even if your primary focus is on a non-model species, begin by running transcript_query using a model species you want to include in your analysis. You need at least two species in Ensembl to allow the script to create the required files and folder structure.

2. Prepare your custom data: Create a CSV file containing your non-model species data according to the format detailed in our documentation. Please refer to the Input Preparation section for guidance: Add Transcripts - Input Preparation.

3. Run add_transcripts: Use this script to incorporate your custom-assembled data into the ThorAxe structure you obtained from the model species analysis.

4. Execute thoraxe: Finally, run thoraxe on the updated dataset that now includes both the model and non-model species data.

Please do not hesitate to contact me if you have any problems during this process or have specific suggestions for improving our documentation. Your feedback is valuable in enhancing our software's user experience and utility.

Looking forward to hearing from you, and best regards,