RepeatScout errors

fripeki · 04-08-2019, 02:19 AM

Hello everybody
I was trying to use RepeatScout. I was following some steps one by one to analyze my sequences.
Here there are the passages:

Repeatscout run: using `fname.fa`

1) `./build_lmer_table -l 15 -sequence fname.fa -freq fname.freq`

2) `./RepeatScout -sequence fname.fa -output fnamescout.fa -freq fname.freq -l 14`

Then the next step would be:

3) `cat fnamescout.fa | ./filter-stage-1.prl> fnamescout_filtered.fa`

but it generated an empty output file .fasta

I checked if `TRF` was installed, then I installed `NSEG`. It could be okay.
What's wrong?

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04-08-2019, 02:19 AM	#1
fripeki Junior Member Location: World Join Date: Apr 2019 Posts: 5	RepeatScout errors Hello everybody I was trying to use RepeatScout. I was following some steps one by one to analyze my sequences. Here there are the passages: Repeatscout run: using `fname.fa` 1) `./build_lmer_table -l 15 -sequence fname.fa -freq fname.freq` 2) `./RepeatScout -sequence fname.fa -output fnamescout.fa -freq fname.freq -l 14` Then the next step would be: 3) `cat fnamescout.fa \| ./filter-stage-1.prl> fnamescout_filtered.fa` but it generated an empty output file .fasta I checked if `TRF` was installed, then I installed `NSEG`. It could be okay. What's wrong? Last edited by fripeki; 04-10-2019 at 06:36 AM. Reason: update