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I'm trying to use simpleaf to build an index for Glycine max (soybean). The genome and gtf files required some preprocessing to get them properly formatted.
I ran the following command (using `sim…
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Hello!
I recently discovered your GToTree and have found it super helpful for my master's project and your clear instillation and instructions have been a huge help in getting it too work on my lap…
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Hi developer,
I just want to make sure I am on the right track to make my own index. Because repbase is not openable, I downloaded the fasta file from GENCODE (Genome sequence, primary assembly (GR…
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Dear author,
Thank you for developing such a milestone software, which greatly accelerates the efficiency of assembly.
I am currently conducting assembly of a large genome of a plant species, whi…
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I have certain coordinates that I would like to map in T2T, but from what I know is that it is still not available a version in ideogram for T2T
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### Main steps for adding new genome and annotation collections
# Genus/species/collection names:
What are the collection types and names? Example:
- Arachis/stenosperma/annotations/V10309.gnm1…
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Hi Cristian,
I was wondering if it is possible to have the polymorphic TE coordinates in all génomes and not only in the ref ? It s quite useful when we map RNAseq and other things to the assemblies …
RRebo updated
1 month ago
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Hi, I am experiencing the same issue as Saya #257
I ran the command:
```
perl vcf2maf.pl --input-vcf input.vcf --output-maf output.maf --ref-fasta /home/usr/Documents/Genomes/NCBI_RefSeq_GRCh38/…
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I want to analyze the output of NanoSim based on simulated_aligned_reads and compare it with the input of the human reference genome from GRCh37 and using the pre-trained human guppy model provided fr…
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Hello, thank you for developing the tool. I am new to WGS analysis and subsequently the tool .I am trying to run it for somatic tumor/control samples. I have installed the tool successfully according …