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univieCUBE / gepard

Genome Pair Rapid Dotter
http://cube.univie.ac.at/gepard
MIT License
61 stars 16 forks source link

matrices #7

Closed duhuipeng closed 2 years ago

duhuipeng commented 2 years ago

Dear author My code is as follows java -cp dist/Gepard-1.40.jar org.gepard.client.cmdline.CommandLine -seq1 ../bmxchrX_seqkit.fa -seq2 ../chrX_seqkit.fa -matrix resources/matrices/edna.mat -word 500 -window 1 -lower 95 -outfile gepard_ref1_vs_ref2_1.png my result as follow image But the human article I refer to is as follows image I'm basically all the same result in the article except for the matrice parameter, can you tell if the question of my matrix parameters, I should have an alignment of such centromeric regions, How to set the matrix parameters to show the article

Best HUipengDU

rattei commented 2 years ago

Display parameters can be adjusted using the command line parameters -lower, -upper, -greyscale. Please make use of these parameters.

rattei commented 2 years ago

You might have missed the fact that gepard provides a graphical user interface. One of its use cases is the visual adjustment of display parameters, for later use on the commandline. We strongly recommend the use of the GUI to find the optimal parameters in this case.