Hi Vasilis,As Peter said, the gaps you see in the padded file derive only from *some* reads, not all. This means that the consensus was not called in these positions. You can imagine the padded file as a reference onto which you could align all your reads, even the few "weird" ones that have some inserts, by simply overlaying reads over the reference. If you try to visualize the alignments in GAP5 for example, you will see what all these "stars" (*) are in the consensus. They are there so that the alignments can be easier to visualize, that's all.
So, if you care only about the final consensus, you can consider the unpadded sequence.
Andrej On 03/17/2015 06:21 PM, lenis vasilis wrote:
Hi Peter, Thank you very much for your very quick reply. In that case, If its possible to have intels, how the unpadded file can be ok? I have to eliminate the intels in my assembly (or to identify them) somehow in order to say that this is the final assembly. I'm really sorry for my ignorance. Vasilis. On Mar 17, 2015, at 5:05 PM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote:On Tue, Mar 17, 2015 at 5:00 PM, lenis vasilis <val1@xxxxxxxxxx> wrote:Hello everyone, I' m using MIRA 4 in order to assemble the mitochondrial dna from sheep. I used referenced guided assembly and in the output I found (among else) one Fasta file that called unpadded which has a full sequence without any gap and a Fasta file that called padded with some gaps (" * " (star) symbol). Which is the difference between padded and unpadded files?The are the same except on has gap symbols in it (positions where some of the reads at that location have an insert).Can I say with secure that the unpadded file is the sequence that I have assembled?If I understand your question, yes. Peter -- You have received this mail because you are subscribed to the mira_talk mailing list. For information on how to subscribe or unsubscribe, please visit http://www.chevreux.org/mira_mailinglists.html
