Question about Trans2Express usage and local plant database

[Karenmagh]

Hello @albidgy ,

Thank you for developing this very useful tool. I just installed it and am running some tests, but I have some questions:

Multiple short-read libraries:
In my project, I have several samples (control and treatment):

Con1_1_P.fastq.gz
Con1_2_P.fastq.gz
Con2_1_P.fastq.gz
Con2_2_P.fastq.gz
Con3_1_P.fastq.gz
Con3_2_P.fastq.gz
Tra1_1_P.fastq.gz
Tra1_2_P.fastq.gz
Tra2_1_P.fastq.gz
Tra2_2_P.fastq.gz
Tra3_1_P.fastq.gz
Tra3_2_P.fastq.gz

I would like to know if it is possible to specify all of them in a single Trans2Express command (how to do it?), or if I should concatenate the fastq files for each group before running the assembly.

Local plant databases and taxonomy:
The default nr.dmnd file is very large. I would like to create a local DIAMOND database using only plant proteomes. I tried:

diamond makedb --in all_plant_proteins.fasta -d plant_proteins_primary.dmnd

But when running Trans2Express, I got the following error:

Opening the database... Error: Options require taxonomy information included in the database. Please use the respective options to build this information into the database when running diamond makedb: taxonomy mapping information (--taxonmap option), taxonomy nodes information (--taxonnodes option)

Could you advise on how to include the required taxonomy information for a local plant-only database so that it works with Trans2Express?

I would greatly appreciate any guidance or recommendations on these points.

Best regards,
Karen.