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- mummerplot results interpretation - Biostar: S
mummer mummerplot alignment bash • 3 4k views ADD COMMENT • link 4 3 years ago by langziv utrif; 70 1 Entering edit mode Aside from the scattered dots, there is a clear vertical line for each contig scaffold It would suggest you have a array of repeats in these contigs Do you see this for every contig you have assembled? Also, you could
- MUMmer plot visualization - Biostar: S
Hi, I am using MUMmer plot to compare between a de novo assembly with reference genome The percent identity between two genomes is more than 99% but when I plot the two genomes with MUMmer plot, the plot (https: ibb co q08xsZw) doesn't look like that Does anyone have any idea? Thanks
- Using MUMmer 3. 9. 4
I am trying to install MUMmer 3 9 4 on Ubuntu, following the instructions given here: https: github com gmarcais mummer blob master INSTALL md When I try to run nucmer, I get this error message: nucmer: error while loading shared libraries: libumdmummer so 0: cannot open shared object file: No such file or directory
- mummer dot plot - Biostar: S
You can use show-coords from MUMmer to check how many bases you should rotate the assembly (should be equal to the size of your small aligned fragment) I would also suggest to use dnadiff which is also part of MUMmer package
- mummer plot interpretation - Biostar: S
I want to know how to interpret the results of mummer plot graph? What is the meaning of different colours in the graph?
- How to modify dot plot in MUMmer 3 for bacteria . . . - Biostar: S
I would recommend using a different dot-plot visualizer for mummer output, one that is interactive and navigable my favorite: https: dnanexus github io dot see also: https: github com topics dotplot
- A Result From Mummer Alignment
I wonder what kind of alignment view you want or you need any specific format to parse with perl or python The usual way I do nucleotide alignment with mummer is following: align the two sequences nucmer -p out seq1 fa seq2 fa filter the results (delta format) delta-filter -g -u 95 out delta > out fil delta
- How to convert MUMmer output to SAM, GFF, or any other . . . - biostars
I am aligning contigs against a reference genome and would like import the output of Nucmer-MUMmer as a track in GBrowse MUMmer uses its own idiosyncratic output formats (delta format), and to my surprise I was unable to find any working parser for Mummer in BioPerl or BioPython
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