Matt Wersebe

Hi Pasi, Yes this did run, thanks! I was a bit confused because nothing was initially writing the output file and I couldn't see it using very much memory. Many Thanks! Matt

Hi Pasi, I am running the final makefasta.awk script. It seems to be running for a while (>1 hr) is that normal? awk -f /home/weider/Programs/LepAnchor/makefasta.awk SC_F1-1A_hap2.fa chr*.apg >LepAnchor_output.fa Thanks! Matt

Hi Pasi, I think I figured it out. The bed file is created by using the output from JoinSingles2All. This is used to make the map.input for CleanMap and then Map2Bed. Also, in the awk snippet -vn=X, the X needs to be changed to whatever chromosome you are working with. The X in the file above should be a number. Makes much more sense now! Matt

Hi Pasi, I am working on getting the input files together for running LepAnchor. I am bit confused about how to get everything in proper order. My output from LM3 is in the from the OrderMarkers module i.e., "java OrderMarkers2 ... chromosome=X ... >orderX.txt" . I then ran the awk snippet: awk -vn=X '(NR==FNR){map[NR-1]=$0}(NR!=FNR && /^[^#]/){print map[$1],n,$2,$3}' snps.txt orderX.txt >orderX_m.input Generating separate input file for each chromosome. Running head on one produces: h2tg000032l...

Hi Pasi, I am working on getting the input files together for running LepAnchor. I am bit confused about how to get everything in proper order. My output from LM3 is in the from the OrderMarkers module i.e., "java OrderMarkers2 ... chromosome=X ... >orderX.txt" . I then ran the awk snippet: awk -vn=X '(NR==FNR){map[NR-1]=$0}(NR!=FNR && /^[^#]/){print map[$1],n,$2,$3}' snps.txt orderX.txt >orderX_m.input Generating separate input file for each chromosome. Running head on one produces: h2tg000032l...

Hi Pasi, Thanks for the update, I will have to take a closer look at this. Cheers and thanks for the insight, ] Matt

Hi Pasi, Great, I have started to re-run these problematic chromosomes. A couple questions. While running OrderMarkers2 to evaluate the order, for selfing crosses does GrandparentPhase=1 need to be provided for each run? Or does this need to only be included during the initial ordering? Same for the scale parameter? Again, thanks for your responsiveness and help in trouble shooting this! Best, Matt

Hi Pasi, Thanks for your message. To make these graphs, I ran OrderMarkers2 once on the map I got from JS2A. I then evaluated the order 3 times, outputting the phased data for LMPlot in the third go of evaluate order. Most individuals are recombining 2 to3 times per LG, and there isn't much deviation away from that (range is 1-7 recombinations per LG). There aren't any outliers in terms of recombinations. I will re-run the ordermarkers2 step with a few different scale to see if that helps. Many thanks!...