[mira_talk] Re: Assembly

  • From: "Bastien Chevreux" <bach@xxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Sat, 3 Oct 2009 16:53:33 +0200 (MEST)

> From: Sharmista Saha
> [...]

The questions you've been asking during the past 10 days are ... a bit 
troubling. Correct me if I'm wrong, but it appears to me that you are an utter 
novice both in Unix and in sequence assembly. Right? Please don't take offense 
as this is no judgement and shouldn't be a hindrance to ask questions (we've 
all been through that stage), but simply an observation.

A valuation however is that you seem to be pretty reluctant to read the 
available documentation, which - please bear with me if I sound a little bit 
peeved - took considerable time and effort to write, trying to be as simple and 
concise as possible for a subject as difficult as sequence assembly. They're 
not perfect, I know, but should help out in 95% of the cases.

Now to your specific question: what you were looking at was the log of the 
assembly, not the results. The log is something a program dumps out so that in 
case of a problem in the program, one can find out what happened.

What you want are the results. As described in the section "Looking at results" 
of the mira usage manual, you will find the results after the assembly in 
subdirectories, namely "<projectname>_d_info" with all kind of files with 
statistics (and other numbers) and "<projectname>_d_results" with result files 
in different formats, ready to be used with other programs. Have a look at 
these.

Now, I would really suggest that you take yourself a cup of tea or two (or 
coffee or whatever), relax and completely read through "mira usage" manual and 
the "how to use with Solexa" manual. Afterwards, reading through the main 
manual would certainly also tell you a lot of things not mentioned in the 
other, simpler and more focussed, manuals. Once you are through, read them 
again. I know that it takes some time upfront, but it quickly pays off 
afterwards when it saves you tons of time and frustration.

Furthermore, if it would be possible for you to find in your surrounding 
someone a bit more experienced, this also could be beneficial for quickly 
finding where you have problems in understanding the subject. Sitting down with 
two people in front of a screen is one of the best ways to find out about new 
things.

Regards,
  Bastien



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