Sequential contig mapping

Question

[rh1234]

Hi,

I am using short read data to map against assemblies as part of a bulk segregant analysis. The result varies significantly for certain contigs based on whether the reference is the individual contig or within the whole assembly.

Is there a tool which would allow me to map the entire short read dataset to each individual contig one after the other? (rather than to the complete assembly)

(i.e. perform the mapping for the first contig whilst ignoring the others and then remap the complete short read dataset to the next contig, then the next etc.)

Thanks.

Answer 1

[lieven.sterck]

There likely is but I would certainly not advise to use them !

The point in these kind of analyses is exactly to not bias your mapping (because that's what you will be doing). Going for mapping on the whole dataset and then afterwards subfilter them might be OK but do the initial mapping against only a single (or subset of ) contigs is not. It means you will force reads to map to a location which is possibly not the best one genome-wide.