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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
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  • $\begingroup$ Is that the only file produced? The .psa format 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. $\endgroup$ – terdon Jul 8 '17 at 15:21
  • $\begingroup$ 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 $\endgroup$ – hhoomn Jul 8 '17 at 15:40
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    $\begingroup$ 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. $\endgroup$ – ithinkiam Jul 11 '17 at 11:45
  • $\begingroup$ 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. $\endgroup$ – hhoomn Jul 11 '17 at 14:09
  • $\begingroup$ @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. $\endgroup$ – ithinkiam Jul 13 '17 at 9:05
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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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