<p>I'm running Repeatscout. I built the l-mer table called myfile.freq of myfile.fa
Can anyone tell me what do they mean the second and third columns produced as output?
here I report an example:</p>

<pre><code>AAAAAAAAGCGGGA  3       107776875 
AAAAAAACTGTATG  10  83440519
AAAAAAAAGGCGTA  3   41037187
AAAAAAACTTGAAT  7   94493612
CATACATGCATGCA  1065    125671338
CATACATGCTTGAA  7   121799834
AAAAAAATCATGCA  10  95493021
AAAAAAAGTCCAGT  3   125127980
AATTCACATGTATG  7   102505668
</code></pre>

<p>I read the tutorial that explains how to run the program: <a href="https://bix.ucsd.edu/repeatscout/readme.1.0.3.txt" rel="nofollow noreferrer">https://bix.ucsd.edu/repeatscout/readme.1.0.3.txt</a>. 
It says: "First, build_lmer_table creates a file that tabulates the frequency of all l-mers in the sequence to be analyzed"</p>

CC BY-SA 4.0
2019-04-29T14:48:15.220Z
Welcome to the site Jonny. Did you read the documentation of the software you are using, or any tutorial where it is used? Did you try searching on the internet for this format/output?
llrs
CC BY-SA 4.0
2019-04-29T15:13:58.737Z
Yes, I searched and I read some manuals but I really don't understand what they mean. I know that it's built this table of l-mer from the original genome fasta file
jonny
CC BY-SA 4.0
2019-04-29T20:11:04.843Z
If you could link and cite what parts you don't understand we could help you better
llrs
CC BY-SA 4.0
2019-04-29T21:15:29.877Z
" First, build_lmer_table
creates a file that tabulates the frequency of all l-mers in the
sequence to be analyzed."  I SUPPOSED that the second column could indicate the number of l-mer, but I don't understand what the third column is showing
jonny
CC BY-SA 4.0
2019-04-29T21:32:41.697Z
Where are you taking this from? Could you provide also the link?  Do not forget to [edit] the question to include this relevant information
llrs
<transposable-elements><repeatmasker>
repeatscout freq table
# repeatscout freq table

(Asked by: username_0 on 2019-04-29)

I'm running Repeatscout. I built the l-mer table called myfile.freq of myfile.fa
Can anyone tell me what do they mean the second and third columns produced as output?
here I report an example:
AAAAAAAAGCGGGA  3       107776875 
AAAAAAACTGTATG  10  83440519
AAAAAAAAGGCGTA  3   41037187
AAAAAAACTTGAAT  7   94493612
CATACATGCATGCA  1065    125671338
CATACATGCTTGAA  7   121799834
AAAAAAATCATGCA  10  95493021
AAAAAAAGTCCAGT  3   125127980
AATTCACATGTATG  7   102505668

I read the tutorial that explains how to run the program: https://bix.ucsd.edu/repeatscout/readme.1.0.3.txt. 
It says: "First, build_lmer_table creates a file that tabulates the frequency of all l-mers in the sequence to be analyzed"

**Tags:** transposable-elements, repeatmasker
> **Comments:**
> **username_1**: Welcome to the site Jonny. Did you read the documentation of the software you are using, or any tutorial where it is used? Did you try searching on the internet for this format/output?  
> **username_0**: Yes, I searched and I read some manuals but I really don't understand what they mean. I know that it's built this table of l-mer from the original genome fasta file  
> **username_1**: If you could link and cite what parts you don't understand we could help you better  
> **username_0**: " First, build_lmer_table creates a file that tabulates the frequency of all l-mers in the sequence to be analyzed."  I SUPPOSED that the second column could indicate the number of l-mer, but I don't understand what the third column is showing  
> **username_1**: Where are you taking this from? Could you provide also the link?  Do not forget to [edit] the question to include this relevant information  

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## 0 answers

