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Hi,
I was thinking about the inverse problem of #306. If we start with a large graph with many samples, we may be interested in subgraphs covered by a subset of those samples (e.g., we build a grap…
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Hello,
I'm following the The Minigraph-Cactus Pangenome Pipeline and managed to complete almost all steps. However, when I ran the cactus-graphmap-join step with command cactus-graphmap-join ./jobs…
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**1. What were you trying to do?**
I made a pangenome using cactus pangenome like this:
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rm -rf js; source /da/cbt/GX/oakeled1/genomes/cyno/pangenome/cactus-bin-v2.6.0/cactus_env/bin/activat…
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Hello,
I've encountered the following error while running a program:
The input file used is the output from minigraph-cactus.
When I created the input VCF using only 3 genome sequences, the c…
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While trying to run the program on a dataset of 200 annotated genomes (gbff, bakta annotated) I got this error:
Traceback (most recent call last):
File "tables/tableextension.pyx", line 1596, in…
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Hi,
I'm getting a segmentation fault when running pgr-mdb. I'm using v0.4.1 downloaded from the releases page running within a docker image generated from: https://github.com/GeneDx/pgr-tk/blob/ma…
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I'm evaluating PPanGGOLiN on MGE genomes and I noticed that some genomes contained multiple genes within the same cluster, which you wouldn't expect for very compact genomes. Upon further investigati…
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Hi,
I am attempting to use pgr-query to search the human pangenome draft. Known exact hits are not being found. For example:
`pgr-query pangenome_draft1_v1.1 test1.fa test1_output`
returns …
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Hello! I am new to pangenome analysis so apologize if this is easily answered elsewhere. I am wondering the best way to extract a slice of a pangenome. I'm currently trying to work with the Minigraph/…
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See https://github.com/nf-core/pangenome/blob/dev/conf/test_full.config#L15