Mappping read to its exact postion in genome

Question

[EVR]

HI,

I would like to map the RNA seq reads to exact position from where it originated in genome USING TOPHAT, how could one achieve that. I am confused with the options -M,-x and -g parameters.How can i amke use these parameters to achieve the output. Kindly guide me

Thanks in advance

Answer 1

[Devon Ryan]

Use the defaults.

[EVR]

Thanks Ryan. How does the multi mappers(reads that map to multiple regions) gets treated ? Alos how to find whether a genome is duplicated so that we can choose parameters according to that. Kindly guide me, please

[Devon Ryan]

Multimappers are given an appropriately low MAPQ. Regarding "duplicated genes", that would depend on whether you want paralogs or CNVs. In either case, just search the site for that.

[GenoMax]

If you don't have a reference genome that is well understood/finished (sounds like you don't: Computing Genome Duplication ) you are going to have to do the best you can.
If the genome duplication (in part of whole) is not real but an artifact of state of your genome then multi-mapping may be an important side effect.