<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>

CC BY-SA 4.0
2018-11-18T08:39:39.300Z
2018-11-18T08:39:39.300Z
winni2k
<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>

CC BY-SA 3.0
2017-07-08T15:21:26.063Z
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.
terdon
CC BY-SA 3.0
2017-07-08T15:40:17.990Z
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
hhoomn
CC BY-SA 3.0
2017-07-11T11:45:54.160Z
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.
ithinkiam
CC BY-SA 3.0
2017-07-11T14:09:01.923Z
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.
hhoomn
CC BY-SA 3.0
2017-07-13T09:05:26.830Z
@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.
ithinkiam
CC BY-SA 3.0
2017-07-13T09:50:46.760Z
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)
hhoomn
<read-mapping><rna-alignment>
How to interpret contig-alignment.psa produced by velvet
# 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:
>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**: @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.  
> **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)  

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## 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.


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