Basic question about concept of contig

[diego diaz]

Hi,

I have a little doubt about the definition of a contig. According to Google, It is a set of overlapping DNA segments that together represent a consensus region of DNA. This description makes sense when we are performing denovo assemblies, but when we are mapping reads to a reference genome, is It correct to call contigs certain regions where several reads were mapped?

Thanks in advance!

[Brian Bushnell]

A contig is a contiguous sequence of defined DNA. The definition you found is incorrect.

When you map, the contigs are already defined in the reference regardless of mapping results. Within the reference, a sequence of letters ACGT bounded on either end by Ns represents a contig.

[diego diaz]

A contig is a contiguous sequence of defined DNA. The definition you found is incorrect.

When you map, the contigs are already defined in the reference regardless of mapping results. Within the reference, a sequence of letters ACGT bounded on either end by Ns represents a contig.

Thanks

This afternoon I had a little discussion about definition of contigs with a person in my lab. He argued that, for example, when we map a set of miRNAs reads to a reference genome, we can extract the regions where the reads were mapped and call these regions contigs, because a set of "contiguous" reads were mapped there. I think this is a wrong concept of contig right?

My concept of contig is similar to that you mentioned.

[Brian Bushnell]

That's correct; contigs are not defined by mapping, they are inherent to the reference.

[diego diaz]

Thanks again