Comments (3)
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.
from chromeister.
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.
from chromeister.
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!
Bests
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Related Issues (20)
- remove the [1] and null device from the stdout of both R scripts
- Comparison of large genomes.. messy plot HOT 9
- compute_score.r error HOT 2
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- Interpretation of scores HOT 1
- coordinates from the events file HOT 4
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- Breakpoint about inversion HOT 2
- Problem with run_and_plot_chromeister.sh
- error cannot open file 'dotplot.mat.csv': No such file or directory HOT 11
- Bad Install due opencv-python HOT 1
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- error of removal of "index-refseq-qryseq.csv" HOT 1
- Whole genome comparisons. HOT 1
- bring chromeister to bioconda and update galaxy tool HOT 20
- Error in axis - no locations are finite HOT 2
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