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Forum: Bioinformatics 07-12-2010, 03:50 AM
Replies: 16
Views: 5,349
Posted By 0Gen
Sequence quality is gradually reduced toward the...

Sequence quality is gradually reduced toward the end of a read.

What is the length distribution of your library molecules? If < 400 bp, it would be OK.

The Titanium libraries are typically 600...
Forum: 454 Pyrosequencing 06-14-2010, 04:13 PM
Replies: 14
Views: 10,376
Posted By 0Gen
Hi, The RL adaptor seems to be a Roche...

Hi,

The RL adaptor seems to be a Roche secret. There is a recent paper uses an Y adatpor + Taqman-MGB qPCR + Poisson distribution.
...
Forum: 454 Pyrosequencing 05-31-2010, 03:24 AM
Replies: 3
Views: 2,312
Posted By 0Gen
Since you mentioned isothermal amplification,...

Since you mentioned isothermal amplification, what method did you use for sample amplification?

I had the same problem - TGs on one side and ACs at the tail (if the tail was not trimmed). My...
Forum: 454 Pyrosequencing 05-31-2010, 12:33 AM
Replies: 42
Views: 13,028
Posted By 0Gen
Hi Nicoras, If your speculation of light...

Hi Nicoras,

If your speculation of light interference between close wells and the problem at the analysis software level are true, these issues should hold true also before Lib-L was introduced?
...
Forum: 454 Pyrosequencing 05-05-2010, 07:42 AM
Replies: 69
Views: 24,200
Posted By 0Gen
Agree! But might need to take into consideration...

Agree! But might need to take into consideration where you are. This paper seems to help a bit in understanding this issue.

http://nar.oxfordjournals.org/cgi/content/full/gkq332
Forum: 454 Pyrosequencing 05-05-2010, 06:53 AM
Replies: 14
Views: 10,376
Posted By 0Gen
This Y adaptor variant might be of interest. ...

This Y adaptor variant might be of interest.

http://nar.oxfordjournals.org/cgi/content/full/gkq332
Forum: Bioinformatics 04-25-2010, 05:20 AM
Replies: 4
Views: 1,470
Posted By 0Gen
Some reads will be overlapping. About one...

Some reads will be overlapping.

About one third locations have 0x coverage, one third 1x, fewer 2x, even fewer 3x ...
Forum: Bioinformatics 04-11-2010, 02:45 PM
Replies: 0
Views: 1,674
Posted By 0Gen
GoldenPath for bacteria?

Hi,

I am working on 454 data of a bacterial genome. I use gsMapping and don't know what is the format of GoldenPath.

I searched the UCSC website and did not find such a file for my bacterium....
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