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estebanpw / chromeister

A dotplot generator for large chromosomes
GNU General Public License v3.0
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Sorting the plot from chromeister #13

Closed harmeet1990 closed 2 years ago

harmeet1990 commented 3 years ago

Hi Is it possible to sort the chromeister plot according to the reference coordinates? I found a thread discussing the same using Mauve but I am dealing with a huge genome and It doesn't work.

Thanks

estebanpw commented 3 years ago

Hello @harmeet1990

CHROMEISTER just compares the query and reference sequences in the given order in the FASTA file.

So I think you would need to reorder the sequences in the reference FASTA file before running the comparison. How do the reference coordinates look like? And how long is each sequence in the reference? (aprox). It maybe can be done with some linux sort pipeline.

harmeet1990 commented 3 years ago

Ya I can sort the fasta but I was hoping for simpler where the Rscript for plotting also sorts the files. I am dealing with bread wheat and each sequence is between 400 to 800 Mb.

estebanpw commented 3 years ago

Unfortunately it cant do that (yet), and I gues you will have to manually sort the files. But its an interesting feature. We will consider including this for a further release!

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