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Description:
I'm encountering an issue when running the following command:
PanGenie-index -v pangenome.vcf -r GXFZ.fa -t 8 -o pangenome
The error message I'm receiving is:
Here, pange…
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Hi there I'm working on a `LaTex` documents where I'm using several `tcolorbox` code blocks for the BASH language. In one of them I happen to have a parameter for a tool of such form: `0.03`. Apparent…
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I have a pangenome with two paths, from which I have created a flattened pangenome (FASTA file) using `odgi flatten`. I also have a bed file with feature coordinates specific to a path. I understand t…
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At 70 genomes and 109GB of graph data
```
-rwxr----- 1 kevin kevin 109G Jun 26 08:10 pangenome.lemongraph
-rwxr----- 1 kevin kevin 8.0K Jun 26 08:42 pangenome.lemongraph-lock
```
Not sure why, …
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Hello,
I used the HPRC pangenome (https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/freeze1/minigraph/hprc-v1.0-minigraph-grch38.gfa.gz) to do the analysis. My processes to …
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Hi
I've just ran a cactus-blast job, based on the cactus-prepare output, using the following command:
```
cactus-blast /cactus/jobStore /data/pangenome_cactus/steps-output/pangenome_guidetree.t…
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Hi!
I'm having some trouble understanding where this can come from.
I tried to align a sequence with HMMER and filter on the e-value at 1e-05.
With HMMER, I have this result in the domtblout:
```
…
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Dear All,
I had read a paper entitled "A pangenome analysis pipeline provides insights into functional gene identification in rice". A very excellent article for pangenome construction in rice, I a…
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Hi
I have a genome graph from Minigraph-cactus I'm trying to create a spliced graph from along with indexes to run vg mpmap with and later rpvg.
I tried running with the GBZ graph directly from …
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I created a pangenome graph using pggb, resulting in gfa and og files. I now wish to perform some mappings to the graph and have a few questions:
1. From the pggb documentation I understand that the …