how to use galaxy tracrRNAFinder

1

downloaded the several bacteria genom fasta files and uploaded to Galaxy Version 0.1.0 and recieved the following result:
No tracrRNAs were found in this genome.
Command: perl TracrHotSpot.pl -in /mnt/SSD/galaxy/dependency_dir/TracrWeb_v4/tmp/dataset_48168.gbff -mfe_cutoff 20 -p_cutoff 0.975 -e_cutoff 20.0 -cd_cutoff 4.0 -tail_cut 204 -tt_skip 40 -around_cas9 3500

even uploaded streptococcus pyogene genom, got the sam result. i think i have not upload the correct file. I don’t which kind of file should be uploaded for tracrRNAs finder?

2

Hi @zhaozq
can you please provide more info? What server do you use? What tool do you use? The main Galaxy tool shed does not have tracrRNA, so I am somewhat confused by your post.
Kind regards,
Igor

3

i used DeepVirome Galaxy Server at the University of Otago . Galaxy thanks

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4

Hi @zhaozq
Thank you for the reply! It seems it is a locally developed software. It is not available in the main and test tool shed. It means it is very unlikely to find a person with experience in this software on this forum. Contact the local support.
Kind regards,
Igor

1 Like
5

thanks for your suggession.

6

Hi, I just started using tracrRNAFinder and I got the same output as you, even when I ran it on SpCas9. Have you resolved the issue, or did you pivot to using other tools? Your response will mean a lot to me!

Below is my result:

No tracrRNAs were found in this genome.

Command: perl TracrHotSpot.pl -in /mnt/SSD/galaxy/dependency_dir/TracrWeb_v4/tmp/dataset_49894.gbff -mfe_cutoff 20 -p_cutoff 0.975 -e_cutoff 20.0 -cd_cutoff 4.0 -tail_cut 204 -tt_skip 40 -around_cas9 3500