Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-11-18T08:39:39.300Z
Answers.LastActivityDate: 2018-11-18T08:39:39.300Z
Answers.UserDisplayName: winni2k
Body: <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>
  
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-08T15:21:26.063Z
Comments.Text: Is that the only file produced? The [.psa format](http://web.expasy.org/pftools/psa.5.html) is not like what you show (I think, anyway, I haven't used it before but that's what I could find). Are there really no other output files? If not, it sounds as though that might be a bug.
Comments.UserDisplayName: terdon
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-08T15:40:17.990Z
Comments.Text: Of course there are other files that also appear while using velvet without the option `-alignment yes`. But related to contig alignment I can only see this file
Comments.UserDisplayName: hhoomn
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-11T11:45:54.160Z
Comments.Text: I don't think velvet is doing what you think it is. Velvet is a genome assembler. To quote the velvetg command help: "-alignments <yes|no> : export a summary of contig alignment to the reference sequences (default: no)" If you want to align RNA-seq reads to a transcriptome and get "gene-expression profiles" use a tool such as bowtie2 or Salmon.
Comments.UserDisplayName: ithinkiam
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-11T14:09:01.923Z
Comments.Text: Thank you, I used Last aligner, but the reason I wanted to use velvet was because It generates coverage ratio that could indirectly imply gene expression.
Comments.UserDisplayName: hhoomn
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-13T09:05:26.830Z
Comments.Text: @hhoomn It does in a very roundabout way and it won't give any measure of relative expression between genes. I think you need to explain what exactly it is you want to do in terms of a biological question. It seems to me you're asking the wrong question, here.
Comments.UserDisplayName: ithinkiam
Comments.ContentLicense: CC BY-SA 3.0
Comments.CreationDate: 2017-07-13T09:50:46.760Z
Comments.Text: The question is that what does this file contain, and the answer is yet unclear, but I solved what I needed to do with another tool, if you want to know what I was doing see [here](https://bioinformatics.stackexchange.com/questions/1019/how-can-i-compute-gene-expression-for-a-set-of-rna-reads)
Comments.UserDisplayName: hhoomn
Tags: <read-mapping><rna-alignment>
Title: How to interpret contig-alignment.psa produced by velvet
ThreadText: # How to interpret contig-alignment.psa produced by velvet
  
  (Asked by: username_0 on 2017-07-08)
  
  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](https://paste.ofcode.org/d9599cGH3aXnbdGqtWqrMs):
  
  ```
  >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
  
  ```
  
  **Tags:** read-mapping, rna-alignment
  
  > **Comments:**
  > **username_1**: Is that the only file produced? The [.psa format](http://web.expasy.org/pftools/psa.5.html) is not like what you show (I think, anyway, I haven't used it before but that's what I could find). Are there really no other output files? If not, it sounds as though that might be a bug.  
  > **username_0**: Of course there are other files that also appear while using velvet without the option `-alignment yes`. But related to contig alignment I can only see this file  
  > **username_2**: I don't think velvet is doing what you think it is. Velvet is a genome assembler. To quote the velvetg command help: "-alignments <yes|no> : export a summary of contig alignment to the reference sequences (default: no)" If you want to align RNA-seq reads to a transcriptome and get "gene-expression profiles" use a tool such as bowtie2 or Salmon.  
  > **username_0**: Thank you, I used Last aligner, but the reason I wanted to use velvet was because It generates coverage ratio that could indirectly imply gene expression.  
  > **username_2**: @username_0 It does in a very roundabout way and it won't give any measure of relative expression between genes. I think you need to explain what exactly it is you want to do in terms of a biological question. It seems to me you're asking the wrong question, here.  
  > **username_0**: The question is that what does this file contain, and the answer is yet unclear, but I solved what I needed to do with another tool, if you want to know what I was doing see [here](https://bioinformatics.stackexchange.com/questions/1019/how-can-i-compute-gene-expression-for-a-set-of-rna-reads)  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2018-11-18. Score: 2
  
  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.
  
  
  ---
  
  