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**Description**
**Sub-lineage of:** BA.2
**Earliest sequence:** 2023-7-24, Denmark
**Most recent sequence:** 2023-7-31; Denmark & Israel
**Countries circulating:** Denmark (2), Israel
**Number of…
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Hello,
I have a draft genome, and RNA-seq long-reads which I used to generate a reference-based transcriptome with StringTie (GTF), and I also created a reference-free transcriptome (FASTA).
I …
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Dear Brian,
I accidentally analysed i.e., assembly and mapping, stranded RNAseq data (dUTP protocol) as unstranded. After noticing, I reanalysed the data set in strand-specific mode. When comparing…
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I'm trying to create a new network, I wrote the .json file. In Python I write:
- config = from_json("CPG_bsb4.json") - OK
- scaffold = Scaffold(config) …
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Hi,
I have a question about the script that does the translation of ORFs to genome coordinates. There are a fair number of sequences that have the error 'shouldn't have a minus-strand ORF on a spli…
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Hi,
We are trying to generate .tbl file for NCBI submission using convert_gff3_to_ncbi_tbl.py script at biocode. But the problem is, GFF3 produced by Transdecoder has multiple genes predicted for s…
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貼吧活動:(請查閱 [SARS-CoV-2 Timeline by 2020.02.21](https://github.com/agorahub/_meta/blob/agoran/theagora/sari/Memorandum_2020-02-21_SARS-CoV-2-Timeline_Nathan.pdf?raw=true), by Nathan :cloud: )
- Colla…
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Hi,
I do not plan to use GeneMark-ET but I want to use Augustus, GlimmerHMM and SNAP.
1. If I ran `funannotate train` do I still have to use `funannotate predict --rna_bam `? If yes then what is …
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Hi,
I performed transdecoder on 13 RNA samples at first, and then included 18 more samples to perform gene prediction with transdecoder. Using the same genome( repeats unmasked), I was able to pred…
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HI,
> If you have RNA-Seq data and have reconstructed transcripts using a method such as [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/) or [PASA](http://pasapipeline.github.io/), you ca…