Closed Silverfoxcome closed 1 year ago
Hi,
Thanks for using our tool and I apologise for my late response. To run it you don't need to call the variable, instead just type:
draw.pairwise("../data/pt_syntenicBlocks.txt", "plotsynteny", "../data/refSizes_pt_ref.txt", "../data/tarSizes_pt_assembly.txt", "B73_PT_Ref", "pt_assembly")
Marta
Hi! @Silverfoxcome Thank you for posting for process. I having the same struggle. I just would like to know, Was It possible to solved it with the advise of @marta-fb? I did the same with the following as output
draw.pairwise("../Desktop/Chromosome_severalSps.txt", "../Desktop/plotsynteny", "../Desktop/refSizes_pt_ref.txt", "../Desktop/tarSizes_pt_assembly.txt", "B73_PT_Ref", "pt_assembly") Error in names(x) <- value : 'names' attribute [2] must be the same length as the vector [1]
Good day :)
Thank you for this useful tool!
I have been trying to do a simple Pairwise Synteny Plot between 2 short genomes (chloroplast genomes, the reference and my assembly) but I should be doing something wrong, because I get this error message:
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [1]
I'd be very grateful if you could help me, please :)
To draw my plot with this function
I started to create the necessary files. In this plot, I just want to select 2 blocks of synteny between my genomes, so I followed the guide to make the file
pt_syntenicBlocks.txt
The first field (chr - chromosome of reference species) ONLY accepts numbers so I just put 1 as the reference genome. This is the tab separed field I created:
I attach it here just in case :) : pt_syntenicBlocks.txt
For reference_chr_size I created a file
refSizes_pt_ref.txt
that only has this information (separated but 1 blank space):I attach it here just in case :) : refSizes_pt_ref.txt
For target_chr_size I created a file
tarSizes_pt_assembly.txt
that only has this information (separated but 1 blank space)I attach it here just in case :) : tarSizes_pt_assembly.txt
I called the library, function and files in the following way:
And I get this error message:
Error in names(x) <- value :
'names' attribute [2] must be the same length as the vector [1]
I would be very grateful if you could help. Thanks a lot in advance :)