Question: Plasmid Detection in the SMRT/PacBios data
0
gravatar for Mohit
4.6 years ago by
Mohit0
India
Mohit0 wrote:

Hello ,

I am using PacBios data for the bacterial genome analysis. I have to find out about the Plasmid DNA. Is there is any plasmid DNA in the final outcome??

Any one knows about it?

 

Thank you!

ADD COMMENTlink modified 4.6 years ago • written 4.6 years ago by Mohit0
0
gravatar for lexnederbragt
4.6 years ago by
lexnederbragt1.2k
Oslo, Norway
lexnederbragt1.2k wrote:

Usually, there is a size selection step during library preparation, removing (reducing) fragments under a certain size. If that cutoff is above the size of your plasmid, it may have been removed. Otherwise, (reads originating from) plasmids will be part of the final dataset or assembly. Beware that the assembly process could potentially result in them being merged to another part of the genome, e.g. (one of) the chromosome(s).

ADD COMMENTlink written 4.6 years ago by lexnederbragt1.2k
0
gravatar for Mohit
4.6 years ago by
Mohit0
India
Mohit0 wrote:

Hi,

Is there any computational method to check that???

I used  UniVec Database For the Confirmation.. But What I think, There are limited sequences in UniVec near about 3K-4K. Now, I am looking for some computational tool which can help me regarding!

 

 

 

Thank you!!!

Mohit

ADD COMMENTlink written 4.6 years ago by Mohit0
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