Bambus mate file

[coldturkey]

Quick question.
I wish to produce scaffolds from my 454 reads which I assembled using Mira.
In the .mate file
library <name> <min><max>
does the name refer to the 454 sff file name ? or is it any name?

[edge]

Hi,

You got the solution about your question before?
I face the same problem like you now
Can give me some advise or solution?
Thanks ya.

Quick question.
I wish to produce scaffolds from my 454 reads which I assembled using Mira.
In the .mate file
library <name> <min><max>
does the name refer to the 454 sff file name ? or is it any name?

[bio-x]

Quick question.
I wish to produce scaffolds from my 454 reads which I assembled using Mira.
In the .mate file
library <name> <min><max>
does the name refer to the 454 sff file name ? or is it any name?

any name you like!

[edge]

thanks a lot.
library <name> <min><max>
Do you have any idea about the min and max refer to?

any name you like!

[bio-x]

thanks a lot.
library <name> <min><max>
Do you have any idea about the min and max refer to?

M=mean of the insert size of your library;
stdv=standard deviation of your library;
min=M-stdv;
maxM+stdv

[edge]

Thanks again ya, bio-x.
Sorry again if I bring you any inconvenience or loosing your time.
Regarding the mean of the insert size and standard deviation of my library.
Can I know which text file I should referred to find out the mean of the insert size and standard deviation?
I still very fresh and can't get a lot of info to fill in the BAMBUS mate file from internet.
Hope that you don't mind to share your experience with me.
I very appreciate and thanks you a lot.

M=mean of the insert size of your library;
stdv=standard deviation of your library;
min=M-stdv;
maxM+stdv

[bio-x]

hi, edge,
"Can I know which text file I should referred to find out the mean of the insert size and standard deviation?"
your text from where? you should ask the seqencing company.

Bio-x

[edge]

Hi bio-x,
do you experience using MIRA?
I face this trouble problem now

http://seqanswers.com/forums/showthread.php?p=9449#post9449

Hope can get your advise.