text: user3793: 
  I am working with RNA-seq data without a reference genome/transcriptome and am instead using a Trinity de novo transcriptome assembly.
  I analyzed both isoform and gene expression abundances using RSEM.
  And got differentially expressed GENES via DESeq2.
  In the next step I want to get fasta sequences of differentially expressed genes to use them in the subsequent BlastX/Blast2Go analyses.
  Considering the fact that my Trinity created assembly is based on isoform id:
  How can I extract the gene sequence out of it? Is that a right thing to combine all the isoforms of a single gene in order to generate the longest possible isoform assembly? 
  If so, how can I do it to have a union-exon (combined form of all the exons present in the isoforms of an individual gene) sequence used in my Blast analysis? 
  If not, how should I proceed with the data type available?
  Trinity assembled file includes the isoform column as:
  TRINITY_DN1780_c0_g1_i2 
  TRINITY_DN1780_c0_g1_i1 
  TRINITY_DN1780_c0_g1_i3 
  TRINITY_DN1780_c0_g1_i4 
  TRINITY_DN1780_c0_g1_i5
  
  and the DESeq2 produces the output (gene differentials) as:
  TRINITY_DN1780_c1_g1
  
  
  
  user2085: From your question it isn't clear if you are trying to identify the isoforms that have a very high or very low differential expression value, or if you are trying to correctly find an orthlog for your top hits using BLAST. 
  If your question is about isoform-level quantification, identifying DE at the isoform level is challenging and DESeq2 is only designed for gene-level analyses. That is why it is only outputting genes rather than a specific isoform.
  
  user77: There's no clear way to go from a trinity "gene" (this is just a cluster of isoforms with shared sequence) to a linear gene sequence that will be blastable and not cause a number of headaches (e.g., due to swapping the order of exons).
  What I would suggest that you do is either Blast2GO the isoforms within the Trinity-defined "genes" or take the highest expressed isoform within a "gene" as the sequence you feed into Blast2GO for that gene. Alternatively just use isoforms for everything and avoid this whole issue.
  
original_text: 3793: <ol>
  <li>I am working with RNA-seq data without a reference genome/transcriptome and am instead using a <strong>Trinity <em>de novo</em> transcriptome assembly</strong>.</li>
  <li>I analyzed both isoform and gene expression abundances using RSEM.</li>
  <li><p>And got differentially expressed GENES via DESeq2.
  In the next step I want to get fasta sequences of differentially expressed genes to use them in the subsequent BlastX/Blast2Go analyses.</p>
  
  <p>Considering the fact that my Trinity created assembly is based on isoform id:</p>
  
  <p>How can I extract the gene sequence out of it? Is that a right thing to combine all the isoforms of a single gene in order to generate the longest possible isoform assembly? </p>
  
  <p>If so, how can I do it to have a union-exon (combined form of all the exons present in the isoforms of an individual gene) sequence used in my Blast analysis? </p>
  
  <p>If not, how should I proceed with the data type available?
  Trinity assembled file includes the isoform column as:</p>
  
  <pre><code>TRINITY_DN1780_c0_g1_i2 
  TRINITY_DN1780_c0_g1_i1 
  TRINITY_DN1780_c0_g1_i3 
  TRINITY_DN1780_c0_g1_i4 
  TRINITY_DN1780_c0_g1_i5
  </code></pre>
  
  <p>and the DESeq2 produces the output (gene differentials) as:</p>
  
  <pre><code>TRINITY_DN1780_c1_g1
  </code></pre></li>
  </ol>
   2085: <p>From your question it isn't clear if you are trying to identify the isoforms that have a very high or very low differential expression value, or if you are trying to correctly find an orthlog for your top hits using BLAST. </p>
  
  <p>If your question is about isoform-level quantification, <a href="https://support.bioconductor.org/p/43395/#43400" rel="nofollow noreferrer">identifying DE at the isoform level is challenging and DESeq2 is only designed for gene-level analyses.</a> That is why it is only outputting genes rather than a specific isoform.</p>
   77: <p>There's no clear way to go from a trinity "gene" (this is just a cluster of isoforms with shared sequence) to a linear gene sequence that will be blastable and not cause a number of headaches (e.g., due to swapping the order of exons).</p>
  
  <p>What I would suggest that you do is either Blast2GO the isoforms within the Trinity-defined "genes" or take the highest expressed isoform within a "gene" as the sequence you feed into Blast2GO for that gene. Alternatively just use isoforms for everything and avoid this whole issue.</p>
  