-
Hi, when i used these codes to build the pangenome, but we didn't obtain .vg file in whole genome, only the chromosome .vg file. how to change these code?
/public/software/singularity-ce-3.11.3/bi…
-
Hi,
I generated the pangenome table with the function query_pangenes. I am using the version v1.2.3.
The header of the table is:
pgID interpChr interpOrd og repGene genome …
-
I get a error stating that a Boolean feature of NumPy has been deprecated since NumPy version 1.20. The file requirements state the version of NumPy must be greater than 1.21.
"FutureWarning:
I…
-
Dear shujun,
Thanks for your great software!
When I used the pangenome pipeline of EDTA, the ratio of LTR Copia and LTR unknown changed.
Is it possible to add related species to the pan-genom…
-
Hello Team,
Thanks for the great tool.
I was trying to plot a region of 1 MB and the code crashes showing "KeyError: 'exon_id'", that doesn't make any sense. Because just by reducing the event leng…
-
Dear Christian,
I am looking forward to working with PhaMMseqs (and PhamClust) but have been running into the error below using the demo genes.faa file, would appreciate any guidance – thank you!
Be…
-
Hi Paolo,
For the same pipeline that work no problem on LSF I get a permission error when running on K8s:
```
[warm up] executor > k8s
[f7/cf7557] Submitted process > irods (ImmHet6564351)
[c3/…
-
I am using vg 1.51.0 to try and call snp and indel (vg call -a) from simulated short-read data mapped to a pangenome using giraffe. The true set is obtained by downsampling from the variation set o…
-
Dear author,
Thank you for this great tool! I would like to know if the default 80% similarity/coverage threshold is aimed at genus-level pan-genome analysis, as I understand that Roary, a tool pri…
-
I am trying to use graph map-split with the following command
`cactus-graphmap-split jobstore test_seqfile.txt first_run.gfa first_run.paf --workDir /bigdata/seymourlab/idiaz026/Citrus_non-coding_…