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Hi,
I want to align the short reads to graph using vg giraffe and get a bam file, but i got the following error report. The VCF and graph (GFA file) were constructed using [PGGB](https://github.com/…
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Hi,
I am running the step-by-step pangenome pipeline and failed at `filter_paf_deletions` in `cactus-graphmap`
Based on this log `Exit reason: MEMLIMIT`, it should be caused by insufficient memo…
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Hi,
My name is Maggs. We recently generated a pangenome graph. We used soft-masked genomes as input. Since then, we revised the masking. The regions that are soft masked differ rather substantiall…
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Hi, I ran pggb to build pangenomes for 10 bacterial genomes (Ecoli). The command is `pggb -i merged.fa.gz -o 10n95p -t 20 -p 95 -n 10 -S -m` and it can work well. But i have some confused with the par…
zwh82 updated
11 months ago
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Hi,
I am getting error when running job with multiple processors.
`-[Arcadia-Science/prehgt] Pipeline completed with errors-ERROR ~ Error executing process > 'ARCADIASCIENCE_PREHGT:PREHGT:build_genu…
onbio updated
2 months ago
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Hi
I've run cactus-prepare to generate a series of commands to walk through as different jobs on my cluster to reduce overall resource overhead.
I can see that cactus-blast and cactus-align gene…
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Hi @glennhickey
I am trying to identify the inversion variants from the VCF file of `minigraph-cactus pangenome pipeline`. The way that comes to my mind is to use the "AT" information in "INFO" to…
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Determine the requirements and potential options for the basis of the Pangenome Annotation RNA-seq pipeline.
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Can you provide a detailed explanation on how to run this process? I am a beginner and don't quite understand. Thank you very much
tttxd updated
1 month ago
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Add Sanger's Roary pipeline to GVL and Galaxy.