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Hi,
I have produced ragoo.fasta file with using soapdenovo2 assembly as the input and a reference genome with its gff file. The command is below:
`ragoo.py genome.fasta ref_genome.fna -m minimap2-m…
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Hi,
I was doing some tests using finder for a large plant genome.
At the end of alignments steps, a *.sortedByCoord.out.sam* and a *_for_psiclass.sam* are created and removed only at the end of th…
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Hi, Thank you for creating and maintaining YaHS. I would like to ask question regarding the following:
After I assembled the genome using yahs, I purged the assembly using purge_dups. I would like to…
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Dear developers:
Hello and recently I was using VG to make a variant graph of a plant species and I want to compare the number of reads of one accession mapped onto the graph-based genome via vg gi…
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It's expensive to re-make the NCBI database and re-generate the core genome alignment every time a build is updated.
- [ ] cache database tables, already aligned assemblies
- [ ] query only newly …
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I'm having trouble figuring out how to filter my BAM so that I can use RSEM to quantify the transcriptome.
1. I've used `rsem-prepare-reference` on my аssembly FASTA and GFF.
```
rsem-prepare-refe…
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Hello MaSuRCA team,
I used MaSuRCA (version: MaSuRCA-3.2.7) to de novo assemble Brassica genomes. However, I meet the following error messeage:
Running locally in 1 batch
compute_psa 2044593 5215…
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I used Syri to compare the two haplotypes，and the alignment method was minimap. However, the results show that there are very few Syntenic regions, and most of them are Inverted regions and Translocat…
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Hi, I am trying to use this software to analyze my MS data. But I'm not sure if the calculation is finished, especially since none of the biotype related results are output.
Here are my input,
BA…
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Hello,
I am trying to run funannotate (version 1.7.4) through docker on a CentOS Linux 7. I get the following error:
"IOError: [Errno 2] No such file or directory: 'p2g_18546/diamond.matches.tab"
…