I noticed that there is an option "removeMarkers" that can be used to remove markers from further analysis in SeparateChromosomes. What are the appropriate marker identifiers for LM2 to recognize?
Thank you,
Qifan
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I noticed that there is an option "removeMarkers" that can be used to remove markers from further analysis in SeparateChromosomes. What are the appropriate marker identifiers for LM2 to recognize?
I ran OrderMarkers with 1,900 markers from one linkage group, the results indicated that the likelihood score is negative (-3929), is it normal?
Also, I noticed there are some markers with high error estimate (>0.4 or <-0.4) and around 700 duplicate markers in the order file. If I want to filter out these markers to improve the order accuracy with evaluateOrder, do I need to use "removeMarkers" option or the "OrderMarkers" module will recognize and remove them automatically (with "minError=0.4" option)?
Thank you,
Qifan
If you would like to refer to this comment somewhere else in this project, copy and paste the following link:
I ran OrderMarkers with 1,900 markers from one linkage group, the results indicated that the likelihood score is negative (-3929), is it normal?
That’s for Pasi to say
Also, I noticed there are some markers with high error estimate (>0.4 or <-0.4) and around 700 duplicate markers in the order file. If I want to filter out these markers to improve the order accuracy with evaluateOrder, do I need to use "removeMarkers" option or the "OrderMarkers" module will recognize and remove them automatically (with "minError=0.4" option)?
much easier to remove all that stuff using a bash script
awk '($5<=0.01)' yourmap.txt |cut -f 1| head -n -1> yourmap2.txt [add some grepping off the duplicated markers — please note I never remove them]
Dear Pasi Rastas:
I noticed that there is an option "removeMarkers" that can be used to remove markers from further analysis in SeparateChromosomes. What are the appropriate marker identifiers for LM2 to recognize?
Thank you,
Qifan
It is a list of numbers x y z e.g. removeMarkers=1 100 10003. You need to know which markers to remove.
BW
F
--
Federico Calboli
f.calboli@gmail.com
Thank you!
Dear Federico Calboli,
I ran OrderMarkers with 1,900 markers from one linkage group, the results indicated that the likelihood score is negative (-3929), is it normal?
Also, I noticed there are some markers with high error estimate (>0.4 or <-0.4) and around 700 duplicate markers in the order file. If I want to filter out these markers to improve the order accuracy with evaluateOrder, do I need to use "removeMarkers" option or the "OrderMarkers" module will recognize and remove them automatically (with "minError=0.4" option)?
Thank you,
Qifan
That’s for Pasi to say
much easier to remove all that stuff using a bash script
awk '($5<=0.01)' yourmap.txt |cut -f 1| head -n -1> yourmap2.txt
[add some grepping off the duplicated markers — please note I never remove them]
java -cp OrderMarkers data=yourdata.linkage alpha=0 evaluateOrder=yourmap2.txt improveOrder=0 > yourmapfinal.txt
--
Federico Calboli
f.calboli@gmail.com
All right, Thank you! So only the first column of the order file is used by the "OrderMarkers" module.
Regards,
Qifan