Answers.Body: <p>You can select “Output BED format” on the tRNAscan-SE server:</p>
  
  <p><a href="https://i.sstatic.net/5Lcv1.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/5Lcv1.png" alt="screenshot"></a></p>
  
  <p>Given the output BED format and your input reference in FASTA format, you can easily generate a FASTA file of tRNA sequences via <a href="https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html" rel="nofollow noreferrer"><code>bedtools getfasta</code></a>:</p>
  
  <pre><code>bedtools getfasta -name -s -fo ‹output.fasta› -fi ‹reference.fasta› -bed ‹tRNAscan-SE-output.bed›
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-14T06:48:04.893Z
Answers.Text: thank you for the respond, but I'm running it locally, and the output options are Secondary, statistics, and shown table. but currently, I have submitted the job to their server, let's wait and see :)
Answers.UserDisplayName: M.Bioinfo
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-11T10:52:58.600Z
Answers.LastActivityDate: 2018-10-11T10:52:58.600Z
Answers.UserDisplayName: Konrad Rudolph
Answers.Body: <p>You can do this using the tools from the <a href="https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate" rel="nofollow noreferrer"><code>exonerate</code> package</a>. I assume you have all the sequences shown in your table in a single, multifasta file. If so, first create a single file per sequence using <code>fastaexplode</code>:</p>
  
  <pre><code>fastaexplode reference.fa
  </code></pre>
  
  <p>This will create one file for each sequence in <code>reference.fa</code>. Now, you can read through the results table, and extract the sequences:</p>
  
  <pre><code>tmpFile=<span class="math-container">$(mktemp)
  awk -F"\t" '{ 
                  if(NR&gt;3){ printf "%s %s ", $1, $2; 
                      if($4&gt;$3){
                          print $3, $4-$3
                      }
                      else{
                          print $4,$3-$4,"-"
                      }
                  }
              }' file | while read name num start len rev; do 
                  fastasubseq "$</span>name".fa <span class="math-container">$start $</span>len &gt; <span class="math-container">$num.fa
                  if [[ ! -z $</span>rev ]]; then 
                      fastarevcomp <span class="math-container">$num.fa &gt; $</span>tmpFile &amp;&amp; 
                      mv <span class="math-container">$tmpFile $</span>num.fa
                  fi
                  done
  </code></pre>
  
  <p>I would suggest you go with <a href="https://bioinformatics.stackexchange.com/a/5199/298">Konrad's approach</a>, however, that looks much cleaner and simpler.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-10-11T12:13:28.893Z
Answers.LastActivityDate: 2018-10-11T12:13:28.893Z
Answers.UserDisplayName: terdon
Body: <p>I believe many of the experts here have gone through this issue,</p>
  
  <p>I have run tRNAscan-SE on my genome to predict all the tRNAs, and have successfully gotten all the tRNA coordinates like start, end and type all  arranged in a table.</p>
  
  <p>My question is how can I convert this result to fasta format as long I have all the details about the tRNA ready?</p>
  
  <p>Is there any tool that I can use to get the fasta sequences of the regions described in my table from the original genome?</p>
  
  <hr>
  
  <p><a href="https://i.sstatic.net/8JAdp.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/8JAdp.png" alt="enter image description here"></a></p>
  
  <pre><code>Sequence                tRNA    Bounds  tRNA    Anti    Intron Bounds   Inf       
  Name            tRNA #  Begin   End     Type    Codon   Begin   End     Score   Note
  --------        ------  -----   ------  ----    -----   -----   ----    ------  ------
  NW_011590950.1  1       36704   36632   Ala     AGC     0       0       40.8    pseudo
  </code></pre>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-10T10:06:42.107Z
Comments.Text: Could you provide the table you are referring? Having some sample data will help us to answer your questions. Do you have the reference genome? Many thanks! BTW, what have you tried? Perhaps manually finding the sequence or something else?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-10T10:33:46.120Z
Comments.Text: I have uploaded the table, unfortunately, the data I'm working on doesn't have a reference.
Comments.UserDisplayName: M.Bioinfo
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-10T10:35:36.367Z
Comments.Text: finding these results just by running tRNAscan on my genome, the table above is my Results, in fact, I need a fasta format has all the tRNA sequence to implemented in another tool
Comments.UserDisplayName: M.Bioinfo
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-10T11:05:08.133Z
Comments.Text: You provided a picture, could you provide text that could be used to copy and paste to make it easier for people to use the information?
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-11T06:22:01.783Z
Comments.Text: I did upload a copy from the data but, when past here doesn't arrange accordingly
Comments.UserDisplayName: M.Bioinfo
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-11T07:05:50.950Z
Comments.Text: I could edit and arrange the data, but consider pasting it and format it using code formatting (that will keep the structure of the data)
Comments.UserDisplayName: llrs
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-11T08:03:42.103Z
Comments.Text: What file did you run tRNAscan on? Do you have a single, multifasta file with the sequences NW_011590950.1, NW_011590951.1, NW_011590952.1 etc?
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-11T10:50:05.577Z
Comments.Text: tRNAscan-SE, when run locally, should also provide you with a FASTA output file, if I remember correctly.
Comments.UserDisplayName: Konrad Rudolph
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-14T05:45:30.470Z
Comments.Text: this is my command, im runing trnascan locally --> tRNAscan-SE -E ../GCDROM.fna -o MytRNA -f MytRna-secondary -mMytRna-statistics                          but the run end up with an errore in phase 3
Comments.UserDisplayName: M.Bioinfo
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2018-10-14T05:46:39.870Z
Comments.Text: Status: Phase I: Searching for tRNAs with HMM-enabled Infernal
  Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan
  FATAL:  Unable to open output file MytRNA
Comments.UserDisplayName: M.Bioinfo
Tags: <fasta><trnascan-se>
Title: convert tRNA coordinates Result to Fasta format
ThreadText: # convert tRNA coordinates Result to Fasta format
  
  (Asked by: username_0 on 2018-10-10)
  
  I believe many of the experts here have gone through this issue,
  
  I have run tRNAscan-SE on my genome to predict all the tRNAs, and have successfully gotten all the tRNA coordinates like start, end and type all arranged in a table.
  
  My question is how can I convert this result to fasta format as long I have all the details about the tRNA ready?
  
  Is there any tool that I can use to get the fasta sequences of the regions described in my table from the original genome?
  
  ---
  
  [![enter image description here](https://i.sstatic.net/8JAdp.png)](https://i.sstatic.net/8JAdp.png)
  
  ```
  Sequence                tRNA    Bounds  tRNA    Anti    Intron Bounds   Inf       
  Name            tRNA #  Begin   End     Type    Codon   Begin   End     Score   Note
  --------        ------  -----   ------  ----    -----   -----   ----    ------  ------
  NW_011590950.1  1       36704   36632   Ala     AGC     0       0       40.8    pseudo
  
  ```
  
  **Tags:** fasta, trnascan-se
  
  > **Comments:**
  > **username_1**: Could you provide the table you are referring? Having some sample data will help us to answer your questions. Do you have the reference genome? Many thanks! BTW, what have you tried? Perhaps manually finding the sequence or something else?  
  > **username_0**: I have uploaded the table, unfortunately, the data I'm working on doesn't have a reference.  
  > **username_0**: finding these results just by running tRNAscan on my genome, the table above is my Results, in fact, I need a fasta format has all the tRNA sequence to implemented in another tool  
  > **username_1**: You provided a picture, could you provide text that could be used to copy and paste to make it easier for people to use the information?  
  > **username_0**: I did upload a copy from the data but, when past here doesn't arrange accordingly  
  > **username_1**: I could edit and arrange the data, but consider pasting it and format it using code formatting (that will keep the structure of the data)  
  > **username_2**: What file did you run tRNAscan on? Do you have a single, multifasta file with the sequences NW_011590950.1, NW_011590951.1, NW_011590952.1 etc?  
  > **username_3**: tRNAscan-SE, when run locally, should also provide you with a FASTA output file, if I remember correctly.  
  > **username_0**: this is my command, im runing trnascan locally --> tRNAscan-SE -E ../GCDROM.fna -o MytRNA -f MytRna-secondary -mMytRna-statistics                          but the run end up with an errore in phase 3  
  > **username_0**: Status: Phase I: Searching for tRNAs with HMM-enabled Infernal Status: Phase II: Infernal verification of candidate tRNAs detected with first-pass scan FATAL:  Unable to open output file MytRNA  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_3 on 2018-10-11. Score: 3 | Accepted answer
  
  You can select “Output BED format” on the tRNAscan-SE server:
  
  [![screenshot](https://i.sstatic.net/5Lcv1.png)](https://i.sstatic.net/5Lcv1.png)
  
  Given the output BED format and your input reference in FASTA format, you can easily generate a FASTA file of tRNA sequences via [`bedtools getfasta`](https://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html):
  
  ```
  bedtools getfasta -name -s -fo ‹output.fasta› -fi ‹reference.fasta› -bed ‹tRNAscan-SE-output.bed›
  
  ```
  
  > **Comments:**
  > **username_0**: thank you for the respond, but I'm running it locally, and the output options are Secondary, statistics, and shown table. but currently, I have submitted the job to their server, let's wait and see :)  
  
  ---
  
  ### Answer by username_2 on 2018-10-11. Score: 1
  
  You can do this using the tools from the [`exonerate` package](https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate). I assume you have all the sequences shown in your table in a single, multifasta file. If so, first create a single file per sequence using `fastaexplode`:
  
  ```
  fastaexplode reference.fa
  
  ```
  
  This will create one file for each sequence in `reference.fa`. Now, you can read through the results table, and extract the sequences:
  
  ```
  tmpFile=$(mktemp)
  awk -F"\t" '{ 
                  if(NR>3){ printf "%s %s ", $1, $2; 
                      if($4>$3){
                          print $3, $4-$3
                      }
                      else{
                          print $4,$3-$4,"-"
                      }
                  }
              }' file | while read name num start len rev; do 
                  fastasubseq "$name".fa $start $len > $num.fa
                  if [[ ! -z $rev ]]; then 
                      fastarevcomp $num.fa > $tmpFile && 
                      mv $tmpFile $num.fa
                  fi
                  done
  
  ```
  
  I would suggest you go with [username_3's approach](https://bioinformatics.stackexchange.com/a/5199/298), however, that looks much cleaner and simpler.
  
  
  ---
  
  