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If nseg is in your $PATH it should be ok. What happens if you just run
Do you get the help for trf printed to screen?
Code:
$ trf
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Hello ,I was able to run this with all commands ,i did not compiled nseg properly...but I could run it then..
NOw, I have data from RepeatMAsker , the repeat library ,but it does not show any transpsosns in my genome...I ran it with RMBlast , do you think running with HMMER ,CROSS_MATCH would make a diff ?
also , any recommendations for transposon analysis ?Comment
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help
Dear yzzhang
Have you resovled this problem? I came accross the same problem!
Originally posted by yzzhang View PostComment
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If you exported the RepeatScout-1 directory to your $PATH, you don't need to write ./filename.prl, you just need to write filename.prl. If you include "./", it will search it in the current directory and maybe that is the problem (just guessing, I'm not a RepeatScout user, this looks more like a shell problem!)
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