Entering edit mode
6.5 years ago
Mehmet
▴
820
Dear all,
First of all this is not a question. I have tried to run RATT tool over a week, and finally I managed to run and received results. I am writing here that If anyone needs help about usage of RATT from generating embl file of each scaffold in an assembly to installation of RATT and usage, I can help.
I would like to thank Alex Reynolds, cpad0112 and Juke-34 for their help.
Perhaps most useful would be to write a tutorial on how to use it - and post that here as a tutorial.
A tutorial would be fantastic. I'm struggling with this program, currently.
OK. I will do as soon as possible.
Please let me know where you are having problems while you are running RATT.
Dear Mehmet, Could you tell us, have you finished manual for RATT? Unfortunately, i have some problems with RATT usage. Thanks
RATT documentation is available. Does it not help?
Sorry for being late. Could you please let me know at which point you need help? At least I can do this until I complete tutorial.
Hello Mehmet, I am late to this thread, but would appreciate some guidance please if you are able to help. I have spent the whole day trying to get this software running after installing PAGIT locally and also using EMBLmyGFF3 to build .embl from augustus output. I try to run this script:
start.ratt.sh ./EMBL query.fa MR_H Assembly reference.faand get this error, which is a listed warning in the RATT documentation.
I am using the reference.fa. Please make sure that the description line of each fasta entry is the same than in the embl file name!
I believe that my files comply. Here is an example of the head of my .embl
XXX; XXX; linear; genomic DNA; XXX; XXX; 124273364 BP.
XX
AC XXX;
XX
AC * _APSI_P001
XX
PR Project:PRJEB1234;
XX
and the fasta
Many thanks in advance of your anticipated help.
Hi Peri,
Sorry for my late reply. Can you try this?