re-running TRASH

[amit4mchiba]

Hi,

Thank you for the tool. I wanted your help to identify HOGs. To run TRASH, I used this command-
TRASH_run.sh Genome.fa --o TRASH_primaryC --simpleplot --par 0 --seqt CEN_sequence.csv

This run well, and I could get all the results including summary files. Based on the .csv file, it could identify the families, and then assigned the annotation. Now, I want to run "HOR" analysis using "--horonly" option. What I have understood is that the "--horclass" option will be the class that is included in the "--seqt" option, right? Is it possible to add a new template for centromere in the CEN_sequence.csv file, and then reuse the previous run to get HOR for a new template.

I tried first running TRASH without "--seqt" option, and as expected, could not get any class assigned to any of the repeats. Next, I then rerun the program providing the same output folder destination, and then use "--seqt" option together with "--horclass" and "--horonly" option, but i could not get run done.

I was wondering if I can first run the program without "--seqt", meaning without identifying any class, and then use the predicted repeats to run HOR identification without the need to identify the repeat seq all over again.

I am so sorry for asking such a confusing question, and will be grateful for your help and advice.

thank you so much,

Amit

[BioOmics]

We have the same confuse. But look like two years, still no answer...