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Hello teacher, could you please help me identify where the problem is?
batmeth2 methyGff --coverage 4 -nC 1 --genome genomic.fa -b5 ../genes.bed5 --body --promoter --GENE --distance 2000 --step 0.0…
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1. The first time, I installed EarlGrey **v4.4.0** and RepeatMasker **v4.16**, and I ran around 50 species using this version. The running time of every species was less than 3 days, and those res…
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### Representating strain or subspecies
As suggested in chado [documentation](http://gmod.org/wiki/Chado_Organism_Module) append it to the species value. So for canonical dicty entry it becomes **Dic…
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I tried deeplasmid on a 100-cpu core node. I used the provided Docker image (billandreo/deeplasmid), and followed your instructions using the command feature_DL_plasmid_predict.sh. I tested on 5 diffe…
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I want to propose to move out the GFF3 and FASTA loaders (and perhaps) others into a `tripal_genome` extension module. This way, core Tripal really is just core code. We could even fold in the Inter…
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## The need
In the case of introns (eukaryotes and some of their viruses), the estimated genomic redundancy can be highly inflated, wrongly indicating that the quality is bad.
## The solution
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Hi, I want to produce a vcf file (for phylogenetic analysis) for 15 whole genome, same-species assemblies. I am following the step-by-step pipeline documented under the heading "Yeast Genome" in Min…
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when run hifiasm (0.16.1), I got the wrong log. I cannot find which part is wrong. please help tell me how to save this problem.
hifiasm: htab.cpp:853: void* mz1_worker_count(void*, int, void*): Asse…
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### Description of the bug
Hi.
I'm encountering an error with the methylsig pipeline when using bwameth aligner. The pipeline runs fine with Bismark, but my mapping is low (~40%) and I want to com…
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I'm trying to use the _VariantAnnotation_ package to annotate a _VCF_ file from [nf-core/sarek](https://github.com/nf-core/sarek) (UCSC style) using _AnnotationHub_ `EnsDb` objects (Ensembl style), wh…