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Hello, I am trying to replicate the generation of the Year1 centromeric satellite and segmental duplication annotations as described for usage with the `contig.inclusion.stats.R`. If I understand corr…
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Table seg_dups is 0-based. When displayed in the "Breakpoints" section, move the first position of each annotation 1nt forward and calculate length as end_coord - start_coord.
Check implications wit…
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mostly a note to self until I can find an example that is conveniently sharable with the algorithmic brains of the GCV team...
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Hi,
No idea of you are still actively supporting this tools, but I was trying to map the segmental duplications, and used your align script to calculate the identities. But after running for a whil…
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### Description of feature
[stainedglass](https://github.com/mrvollger/StainedGlass) is particularly useful for disentangling tandem repeat structures and segmental duplications. Under the hood, it…
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I wonder how to parse the MCScanX-transposed (.pairs or .genes) output to obtain the final summary of the different mode of duplications.
For example. below is segmental duplication output segment…
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Hello @freeseek
Is this a known issue that coordinates for CNV loci may be incorrectly/differently presented via SourceSeq mapping workflow?
Since I have large set of chips and samples to analy…
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Does `last` have the ability to efficiently compute self-alignments? `lastz` has a mode specifically for this, but I was hoping to be able to replicate that more rapidly with `last`.
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Using karyoploteR to plot each chromosome with TE locations and coverage for each sample
Want: Graph of each chromosome, with locations of TEs marked and coverage graphs above