Entering edit mode
4.0 years ago
life99945
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20
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!
NW_XXXXXX are generally unplaced genomic scaffold. Try align as sometimes we don't know without analysing the data.
Are you meaning to align nw to nc?