[mira_talk] Re: Assembly

  • From: Sharmista Saha <sharmistasaha@xxxxxxxxxxxxxx>
  • To: mira_talk@xxxxxxxxxxxxx
  • Date: Sat, 3 Oct 2009 20:59:49 +0530

Thanks a lot for the advice and the guidance . You are absolutely right. I
am  novice to sequence assembly process. This is the first time I am coming
across that (exclusively bioinformatically); and unix also I have not much
experience.  Since I am solely handling the project  myself, so many things
I need to get clear (maybe from the scratch).  May be the questions seems to
be too trivial in your case, but handling for the first time, makes you feel
it quite complex and challenging.  Thus, I had to take your assistance.

If i have bothered you too much, I am really sorry. But, if you do not have
queries how will you learn, is what I feel. I think that is an achievement
to strengthen one's  knowledge. Maybe I have overlooked many important
things with the deadline for each things you have been provided here at
every step. but on the  process tried to learn as much as I can  via direct
interaction with great people like you . Sorry again, for any sort of
inconveniences aroused on the process.

Thanking you,
Regards,
Sharmistha




On Sat, Oct 3, 2009 at 8:23 PM, Bastien Chevreux <bach@xxxxxxxxxxxx> wrote:

> > 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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