Comments (4)
brettChapman
commented on August 11, 2024
Is there any way to add genomic coordinates to the 1D graph image, much like mashmap produces coordinates from a pairwise alignment? We could potentionally provide a chosen reference path to refer to the genomic coordinates for the visualization. At the moment this is a bottleneck for further analysis we're carrying out based on the 1D pangenome graphs, like the ones I provided earlier above. Alternatively, is there a tool I can use on the PAF files generated during the PGGB run which could help. Thanks.
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ekg
commented on August 11, 2024
Totally agree. We need to force a reference order and/or show the reference
order more clearly in the odgi viz view.
To not get blocked though, I'll suggest something already ready:
I usually use the 2D plots like this to understand pairwise relationships.
You can obtain them using odgi untangle, which optionally writes PAF
format. You'll need to choose the target and query paths.
…On Thu, Jan 20, 2022, 09:34 Brett Chapman ***@***.***> wrote:
Is there any way to add genomic coordinates to the 1D graph image, much
like mashmap produces coordinates from a pairwise alignment? We could
potentionally provide a chosen reference path to refer to the genomic
coordinates for the visualization. At the moment this is a bottleneck for
further analysis we're carrying out based on the 1D pangenome graphs, like
the ones I provided earlier above. Alternatively, is there a tool I can use
on the PAF files generated during the PGGB run which could help. Thanks.
[image: Morex_v2_chr1H_ZDM02064_v1_chr1H_pangenome_1H_pctid-95]
<https://user-images.githubusercontent.com/8529807/150301596-68b1d61f-efca-4f88-88fd-cef8ccc2c0c1.png>
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brettChapman
commented on August 11, 2024
Thanks @ekg, I look forward to seeing something implemented in PGGB.
For now I'm using odgi untangle to get the PAF files and then I'm visualising the chromosome coordinates of inversions and gaps in the reference using dot plot tools such as D-Genies, to come up with a scale to overlay on the 1D pangenome graph plots. We're currently writing up a paper, and having a scale to refer to in the figure is essential. Thanks.
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subwaystation
commented on August 11, 2024
@brettChapman there is now a method to sort a graph with odgi by a given reference path or by given reference paths. See https://odgi.readthedocs.io/en/latest/rst/tutorials/sort_layout.html#visualize-the-mhc-by-path-position.
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Related Issues (20)
- seqwish std::invalid_argument error HOT 11
- Error with the __glibc package when installing HOT 5
- Mapping k-mers and contigs to pangenome graph HOT 1
- Flag could not be matched: temp-dir HOT 3
- How to understand the long range links? HOT 5
- smoothxg: Command terminated by signal 4 HOT 3
- PGGB discarding SNPs and Small InDels HOT 4
- add version HOT 1
- Sample command from README.md fails and fix? HOT 2
- Command terminated by signal 4 HOT 8
- Error following tutorial for PGGB VCF evaluation HOT 5
- Building a genus pangenome case HOT 1
- Setting -n to number of genomes, or number of genomes minus one? HOT 3
- empty VCF after running PanGenIe on the pggb assembly HOT 1
- GFA with no P lines HOT 5
- DRB1-3123 example not producing a nice graph anymore after `biwflambda` update. HOT 5
- PGGB use case with hexaploidy genomes HOT 1
- force reference output in VCF HOT 2
- Three chromosome take too long time HOT 16
- High heterogeneity in sequences identity HOT 2
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