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I've installed Repeatscout from https://bix.ucsd.edu/repeatscout/. I've also installed TRF and nseg required by the program. I followed the steps:

build_lmer_table -l 16 -sequence ~/file_fasta/od_1000.fa -freq od_1000.freq

 RepeatScout -sequence od_1000.fa -output od_1000_repeats.fa -freq od_1000.freq -l 16

and the I put this command:

cat od_1000_repeats.fa| filter-stage-1.prl >od_1000_repeats_filt1.fa

but this message appears:

bash: filter-stage-1.prl: command not found...

Why? It is all correctly installed, I can't understand the problem

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1 Answer 1

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If you're in the RepeatScout directory you need to execute the Perl script with a ./ prefix, like so.

cat od_1000_repeats.fa | ./filter-stage-1.prl > od_1000_repeats_filt1.fa

If you're not in the RepeatScout directory, you need to provide the full relative or absolute path when executing the script. Alternatively, you can put the RepeatScout directory in your $PATH environmental variable.

These are all standard UNIX/Linux concepts that many bioinformaticians take for granted, for better and for worse. If you're lost in all the terminology, a crash course in UNIX basics is probably where you would want to start.

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  • $\begingroup$ I installed repeatscout on my PC, I created the Repeatscout directory and It worked without errors. The problem is that it can't execute a file larger more than 800 mb in a 16 gb ram of my pc. So I had to use the cluster but I don't know where is the Repeatscout directory.(If I put "locate Repeatscout" I don't find it). I would to find the path to check if all the programs are correctly installed.. $\endgroup$
    – jonny
    May 1, 2019 at 17:18
  • $\begingroup$ It sounds like you need to get some help from your system administrator. $\endgroup$
    – Daniel Standage
    May 1, 2019 at 18:12

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