[mira_talk] Re: awkward letters in assembled data
- From: Visam Gültekin <teutara@xxxxxxxxxxx>
- To: Mira Talk <mira_talk@xxxxxxxxxxxxx>
- Date: Thu, 29 Sep 2011 21:13:59 +0300
Hi Peter,
That is one rapid replyé Thank you.
Reads' length vary from 111-322 bases.
"You could also show use the first (five) reads, or at least their IDs" i did
not understand this part.
" Perhaps you are seeing IUPAC ambiguity codes?"
You are so right! IUPAC ambiguity codes absolutely did not come to my mind. I
checked the files and i can only find IUPAC codes as unexpected.
That is the beauty of brain storms ( well, this might not fit into the
definition though)
BTW, i checked the mira manual and B.C. added " -CO:fnicpst " for this kind of
issues.
Thank you again and again..
> Date: Thu, 29 Sep 2011 18:54:58 +0100
> Subject: [mira_talk] Re: awkward letters in assembled data
> From: p.j.a.cock@xxxxxxxxxxxxxx
> To: mira_talk@xxxxxxxxxxxxx
>
> 2011/9/29 Visam Gültekin <teutara@xxxxxxxxxxx>:
> > Hi,
> >
> > I have been using mira for a while, and i am pretty satisfied. I did some
> > genome assemblies, everything went well.
> > Right now i have to assemble some EST data that i do not know which
> > technology has been used for sequencing.
> >
> > First of all, is there any suggestion for this kind of data?
> >
> > (by changing file name and some little tweak on command, i did some trial
> > for different tech. There is no big difference)
>
> Do a histogram of the read lengths, that would be a big clue.
>
> What file format are your reads in?
>
> You could also show use the first (five) reads, or at least their IDs,
> that is often enough for a good guess.
>
> > For the next issue, after assembly i manually checked the result files.
> > There are "wwww" "rqk" etc. awkward letters in contigs. How is that
> > possible. I am lucky that i checked and realized that in results,
> > otherwise..
>
> Perhaps you are seeing IUPAC ambiguity codes?
>
> Peter
>
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