Hello Peter, I would like to ask you and something else that I noticed. I converted the maf out into sam and the sam into bam by using your maf2sam.py script as I said. I tried to convert this bam file into fastq and I noticed that includes reads only from one strand. In order to construct this consensus I have used paired and reads, but as it seems Mira mapped only the reads from the first strand. Why is that? Could you check the manifest file that I'm sending you in order to be sure that I wrote it alright? Thank you very much for one more time, Vasilis.
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manifest_lane6.conf
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On Mar 18, 2015, at 7:44 PM, lenis vasilis <val1@xxxxxxxxxx> wrote: > Yes, they are very similar, only 3-5 bases are mismatching. > The problem is that there are some regions with low coverage and some others > that I have picks with around 50% with one letter and around 50% with other. > I don't know if this is based on assembly- mapping error or a pcr error. > > On Mar 18, 2015, at 7:28 PM, Peter Cock <p.j.a.cock@xxxxxxxxxxxxxx> wrote: > >> On Wed, Mar 18, 2015 at 7:12 PM, lenis vasilis <val1@xxxxxxxxxx> wrote: >>> Hi, >>> >>> Thank you very much for your support. >>> I did the conversion by using the maf2sam.py, the script that you have in >>> your blog. >> >> OK, that should work too - I updated it to cover the current MIRA >> file format. >> >>> Now, at the moment I'm trying to identify how the unpadded file >>> filled the gaps from the padded one. >> >> Browsing the assembly in Tablet/IGV should help give you >> a feel for the inserts and how padded versus unpadded >> output from MIRA is a different representation of the same >> assembly. >> >>> I used Mira three times with the data of three different lanes. >>> The three unpadded consensus are different in 3-5 bases only. >>> If the assembly was alright I suppose that these three consensus >>> should be exactly the same, shouldn't be? >> >> No. If you are very very lucky, then maybe. Even assuming >> the DNA that went into the three lanes was the same, you will >> have different errors in the reads, so there is no guarantee >> the three assemblies will give you identical contigs. I would >> expect the ending points of the contigs to differ slightly, >> and in lower coverage regions apparent SNPs between >> the three assemblies seem quite likely. >> >> But at a high level, the three assemblies should be very similar. >> >> 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 > > > -- > 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
