Pasi Rastas

Dear Huan, Thank you for your question. Getting markers into right number of groups can be difficult. There are many discussion threads that might help here. First of all, always make sure that your family structure is correct! Then make sure to use distortionLod=1 (or filter distorted markers in other ways). This should make the marker assignment more robust. With 400 individuals in one family, you could use a lodLimit of about 40. And you can always use both families to assign markers as well if...

Dear Huan, The squeeze removes map positions from the map ends if there are no support for them, basically making the map start at 0cM. Cheers, Pasi

Dear Huan, Thank you for your question. Having this kind of map data is normal. My understanding is that there are transposable elements and other repeats that make some markers map into wrong chromosomes and places. This can be fixed by removing markers in the wrong chromosomes. I don't know how much such markers affect other analysis, but these stand out in linkage maps. Addition to these "jumping" markers, within chromosomes the map data is not necessary informative enough to put all markers into...

Dear Xuemei, Yes, 00 is missing data. sexAveraged=1 only puts average map position to the output maps. It does not change the algorithms in any way. The same effect can be obtained by calculate the average map position from the output of LM3 with sexAveraged=0. Cheers, Pasi

Dear Xuemei, The data is in the input file (p_fil.call)? If you want to call genotypes from it, there is the simpleConvert.awk script to make the calls. LM3 uses all markers as default. You can use informativeMask parameter to use only some subsets of them (e.g. only male informative informativeMask=1, male only + both=13, female only=2, etc.). Cheers, Pasi

Dear Xuemei, The usePhysical will use the contig/pos information from your markers as well as the calculated LOD scores between markers. It will decrease calculated LOD value between markers from different contigs (chromosomes) or optionally between markers too far away in the same contig. This is to obtain linkage groups with the help of LOD scores and the physical location of markers. This might be useful if you have a very few individuals in the mapping cross but a good genome. Cheers, Pasi

Dear Xuemei, The usePhysical will use the contig/pos information from your markers as well as the calculated LOD scores between markers. It will increase calculated LOD value between markers from different contigs (chromosomes) or optionally between markers too far away in the same contig. This is to obtain linkage groups with the help of LOD scores and the physical location of markers. This might be useful if you have a very few individuals in the mapping cross but a good genome. Cheers, Pasi

Dear Felix, proximityScale is in OrderMarkers2. Cheers, Pasi