tRNA input from tRNAscan-SE ?

MoradMMokhtar / MegaLTR

In this study, we introduce MegaLTR, a robust online server that identifies intact LTR -RTs in any target genome, and its local standalone version. MegaLTR is freely available at https://bioinformatics.um6p.ma/MegaLTR

GNU General Public License v3.0

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tRNA input from tRNAscan-SE ? #1

Closed V-JJ closed 1 year ago

V-JJ commented 1 year ago

Hello!

Thanks for the software, it looks great!

I would like to ask whether the tRNAs predicted by "tRNAscan-SE" software can be used as an input to the software.
We are working with a non-model arthropoda species, so our set of tRNAs is entirely predicted. However, we applied some filters to refine the data and retain only the high confidence set of tRNAs.

Thanks in advance, Vadim

MoradMMokhtar commented 1 year ago

Hello Vadim Thanks for using MegaLTR Yes, you can use tRNAs predicted by "tRNAscan-SE" as input if you using the standalone version, while in the webserver this option is not allowed. To use your own tRNA file you have to copy the tRNA fasta file to the bin/tRNA folder and use the option " -T your_fasta_file_name_with_theextension". Please replace the space in the file name with "" or "-" because space is not allowed in the file name.

V-JJ commented 1 year ago

Great! The first test finished successfully! Thanks!