text: user872: I'm using velvet to align given reads of RNA to given CDSs (i.e. coding areas and genes) of an organism, so I can generate gene-expression profiles. But after using velvetg out-dir/ -alignment yes, velvet produces contig-alignment.psa which is a file in a strange format. 
  The file for every contig contains zero or more records of 7 integers, and I cannot understand their meaning.
  The following is an excerpt of the file, and you can see the entire file here:
  >contig_1
  1    193    1939    1939    6   194 2
  195 244 1   1   6   22  71
  >contig_2
  1   84  1   1   6   59  142
  86  170 1935    1935    6   22  106
  172 285 1935    1935    6   108 221
  >contig_3
  1   98  2   2   6   1   98
  100 321 2   2   6   100 321
  334 415 1204    1204    6   1   82
  >contig_15
  1   23  3   3   6   84  106
  
  
  user492: It looks like you are trying to do a transcript isoform expression analysis. Velvet is a genome assembler, and really not designed for this task. The tools you are looking for are kallisto and salmon.
  
original_text: 872: <p>I'm using velvet to align given reads of RNA to given CDSs (i.e. coding areas and genes) of an organism, so I can generate gene-expression profiles. But after using <code>velvetg out-dir/ -alignment yes</code>, velvet produces <code>contig-alignment.psa</code> which is a file in a strange format. 
  The file for every contig contains zero or more records of 7 integers, and I cannot understand their meaning.</p>
  
  <p>The following is an excerpt of the file, and you can see the entire file <a href="https://paste.ofcode.org/d9599cGH3aXnbdGqtWqrMs" rel="nofollow noreferrer">here</a>:</p>
  
  <pre><code>&gt;contig_1
  1    193    1939    1939    6   194 2
  195 244 1   1   6   22  71
  &gt;contig_2
  1   84  1   1   6   59  142
  86  170 1935    1935    6   22  106
  172 285 1935    1935    6   108 221
  &gt;contig_3
  1   98  2   2   6   1   98
  100 321 2   2   6   100 321
  334 415 1204    1204    6   1   82
  &gt;contig_15
  1   23  3   3   6   84  106
  </code></pre>
   492: <p>It looks like you are trying to do a transcript isoform expression analysis. Velvet is a genome assembler, and really not designed for this task. The tools you are looking for are kallisto and salmon.</p>
  