merge LGs to one

[Felix]

Hi Pasi,
Thank you for your help, I have constructed a nice map. For another family, I got some problems:

   1. After OrderMarkers2, I find some LGs pointing the same chromosome. For example, markers of LG1 and LG2 both come from CHR6, makers of LG3 and LG4 both  come from CHR4. I want to merge LG1 and LG2 to one linkage map instead of giving up one of them. I read your previous posts, you said they can manually splice two LGs.  But how do I  calculate the genetic distance of the gap between two LGs, because both of the LGs are from 0cM to xxcM. There are some modules of LM3 can merge this two LGs?
   2. Usually, when separating LGs after SeparateChromosomes2, I want to kown the  genomic coordinates of  markers of each LG, there are some method can do it like the awk after OrderMarkers2 ?

Thank you very much,
Felix

[Pasi Rastas]

Dear Felix,

Thank you for your questions.

1. I think it is easiest to join these linkage groups before OrderMarkers2, e.g. changing 2=>1 in the map file and re-run OrderMarkers2. (Probably you could try to put the markers in these linkage groups next to each other, but you have to try all 4 different orientations, run OrderMarkers2 with evaluateOrder on each of these and pick the one that makes most sense =? highest likelihoods.)
2. I typically use paste command for this. If you have the snps.txt file and the map file from SeparateChromosomes2 (map.txt), just do

paste snps.txt map.txt

or maybe in your case the following

paste snps.txt map.txt|awk '($3 > 0 && $1=="CHR1")'

The snps.txt can be obtained as instructions in the wiki.

Cheers,
Pasi