text: user2328: Hello I made a blastX research  (A query genome in nucleotide format translated into protein in 6 reading frames against a protein dabatase) 
  And here is a head of the result : 
  IDBA_scaffold_7517  493 YP_009316100    0.360   61  27  1   150 4   126 186 6.775E-03   37
  IDBA_scaffold_29149 519 AIG51500    0.428   35  18  1   2792    2896    392 424 2.712E-03   40
  
  I have 2 hits: 
  The first one is the query IDBA_scaffold_7517 that have a hit with a protein sequence YP_009316100 in the (-) strand because the start begins by 150 and ends with 4. 
  The seconde one is the query IDBA_scaffold_29149 that have a hit with a protein sequence AIG51500 in the (+) strand because the start begins 2794 and ends by 2893.
  so with that I actually created a bed file in order to extract the fasta sequences from my genome ( I assume that since there is a hit with a protein in the Genomes the coordinates of this hit should be in a good ORF (without stop codon). 
  Here is the bed_file I made : 
  IDBA_scaffold_7517  4   150 Species 0   -
  IDBA_scaffold_29149 2794    2893    Species 0   +
  
  Then in order to extract the sequences from the coordinates in the Genome I used:
  bedtools getfasta -fi Genome.fa -bed bed_file -s -fo test
  
  with -s to force strandedness. If the feature occupies the antisense, strand, the sequence will be reverse complemented.
  But when I do that the sequences extracted from the query are not in the good ORF. 
  I guess it is because I should take into account the fact that the coordinates are from nuc translated to portein but how could I do that? Should I change the coordinates manually from the bed file according to the fact that it is a negative of positif strand ? 
  Thank you for your help. 
  
  user6251: Blast uses a 1-based coordinate system. Bed is 0-based half open. Your code needs to convert appropriately. See for example: https://www.biostars.org/p/317112/ .
  
original_text: 2328: <p>Hello I made a <code>blastX research</code>  (A query genome in nucleotide format translated into protein in 6 reading frames against a protein dabatase) </p>
  
  <p>And here is a head of the result : </p>
  
  <pre><code>IDBA_scaffold_7517  493 YP_009316100    0.360   61  27  1   150 4   126 186 6.775E-03   37
  IDBA_scaffold_29149 519 AIG51500    0.428   35  18  1   2792    2896    392 424 2.712E-03   40
  </code></pre>
  
  <p>I have 2 hits: </p>
  
  <p>The first one is the query <code>IDBA_scaffold_7517</code> that have a hit with a protein sequence <code>YP_009316100</code> in the <code>(-)</code> strand because the start begins by <code>150</code> and ends with <code>4</code>. </p>
  
  <p>The seconde one is the query <code>IDBA_scaffold_29149</code> that have a hit with a protein sequence <code>AIG51500</code> in the <code>(+)</code> strand because the start <code>begins 2794</code> and <code>ends by 2893</code>.</p>
  
  <p>so with that I actually created a bed file in order to extract the fasta sequences from my genome ( I assume that since there is a hit with a protein in the Genomes the coordinates of this hit should be in a good ORF (without stop codon). </p>
  
  <p>Here is the <code>bed_file</code> I made : </p>
  
  <pre><code>IDBA_scaffold_7517  4   150 Species 0   -
  IDBA_scaffold_29149 2794    2893    Species 0   +
  </code></pre>
  
  <p>Then in order to extract the sequences from the coordinates in the Genome I used:</p>
  
  <pre><code>bedtools getfasta -fi Genome.fa -bed bed_file -s -fo test
  </code></pre>
  
  <p>with <code>-s</code> to force strandedness. If the feature occupies the antisense, strand, the sequence will be reverse complemented.</p>
  
  <p>But when I do that the sequences extracted from the query are not in the good ORF. 
  I guess it is because I should take into account the fact that the coordinates are from nuc translated to portein but how could I do that? Should I change the coordinates manually from the bed file according to the fact that it is a negative of positif strand ? </p>
  
  <p>Thank you for your help. </p>
   6251: <p>Blast uses a 1-based coordinate system. Bed is 0-based half open. Your code needs to convert appropriately. See for example: <a href="https://www.biostars.org/p/317112/" rel="nofollow noreferrer">https://www.biostars.org/p/317112/</a> .</p>
  