<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>

CC BY-SA 4.0
2019-11-14T12:58:48.833Z
thank you very much !
Grendel
CC BY-SA 4.0
2019-11-14T12:55:16.113Z
2019-11-14T12:55:16.113Z
Timur Shtatland
<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>

<fasta><bedtools><orf>
Bedtools get fasta and ORF from a blastX run
# Bedtools get fasta and ORF from a blastX run

(Asked by: username_0 on 2019-11-14)

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.

**Tags:** fasta, bedtools, orf

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## 1 answers

### Answer by username_1 on 2019-11-14. Score: 2 | Accepted answer

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/> .

> **Comments:**
> **username_0**: thank you very much !  

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