Question: Do I Need To Perform Scaffolding For Reference Based Assembly Result ?
1
gravatar for vibhanim.21
6.5 years ago by
vibhanim.2140
Manipal University
vibhanim.2140 wrote:

i had performed reference assembly using MIRA and had got only one single contig. now i have a doubt whether should i perform scaffolding for my data.. ?

assembly reference scaffolding • 2.0k views
ADD COMMENTlink modified 6.5 years ago by Michael Dondrup46k • written 6.5 years ago by vibhanim.2140
1
gravatar for Michael Dondrup
6.5 years ago by
Bergen, Norway
Michael Dondrup46k wrote:

No, you can't scaffold one contig, you need at least two contigs. Also with reference based assembly, the reference sequence will guide the order of potential contigs and doesn't require scaffolding. If you wish to know if your result is valid or not we need more information from you. If the length of the single contig is about the length of the reference, that is a good sign.

ADD COMMENTlink written 6.5 years ago by Michael Dondrup46k

the length of my contig is 2693504 bp and that of reference is 2692570 bp . i think this is good ...

ADD REPLYlink written 6.5 years ago by vibhanim.2140

your contig is almost 1kb longer than the reference, any idea why?

ADD REPLYlink written 6.5 years ago by Michael Dondrup46k

i have no idea why... is this a bad result ?

ADD REPLYlink written 6.5 years ago by vibhanim.2140
2

Google suggests your reference may be http://www.ncbi.nlm.nih.gov/nuccore/NC_016912.1 :-) If the reference is circular, maybe the end of your contig overlaps 1 kb with the beginning?

ADD REPLYlink written 6.5 years ago by lexnederbragt1.2k

Yes, good point, I think that is the reason, so you can scaffold it! With itself.

ADD REPLYlink written 6.5 years ago by Michael Dondrup46k

thank you i will try scaffolding within itself .

ADD REPLYlink written 6.5 years ago by vibhanim.2140
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