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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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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
Here are nine questions we think about, in roughly the order they matter, before...06-18-2026, 07:11 AM -
Data variability is still an issue in sequencing technologies despite the advances in reproducibility and accuracy of these platforms. But the problem does not originate in the sequencing itself, but in the previous steps, before the sample reaches the sequencer.
The first step is collection, followed by preservation and sample preparation for analysis. Most scientists overlook those steps, but not being careful might just be skewing the experiment’s results.
...06-02-2026, 10:05 AM
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