Question: wgs supercontigs (NW_XXXXXX)
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gravatar for life99945
10 weeks ago by
life9994520
life9994520 wrote:

Hi,

I have paired end reads which I mapped to a reference genome. This genome contains two types of contigs. First are contigs with NC identifiers, which represent chromosomes and second type are contigs with NW(NW_XXXXXX) identifiers, which should be supercontigs with gaps.

The questions are: What are these NW contigs? Are they a part of NC contigs or independent units? What should I do when one end of paired end read aligns bouth to NW and NC contigs and another aligns only to NC?

Thank you!

mapping wgs supercontigs • 88 views
ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by life9994520

NW_XXXXXX are generally unplaced genomic scaffold. Try align as sometimes we don't know without analysing the data.

ADD REPLYlink written 10 weeks ago by devarora150

Are you meaning to align nw to nc?

ADD REPLYlink modified 10 weeks ago • written 10 weeks ago by life9994520
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