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Richard raised that it would be nice to add genome annotations to ENA submissions. We discussed on dev call, if we do this, we could potentially also make the annotations available from Loculus direct…
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We should make our two main subworflows (``GENOME`` and ``GENOME_AND_ANNOTATION``) into workflows, as it makes more sense for the structure and modularization of the pipeline (we cannot use subworkflo…
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Hello, I'm sorry to bother you. May I know how to do transcriptome prediction now that I only have full-length transcriptome data?
I have seen many articles on downstreaming the data and then using …
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I could not get the chromsizes.tsv data from human. It there anyone could help? thanks in advance.
scenicplus prepare_data download_genome_annotations --species "hsapiens" --genome_annotation_out_fna…
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Another way we discussed to assess annotation quality is to look at overlapping genes, sense and antisense.
You would expect that similar genomes would have the same rate of these classes, if not, t…
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Hi,
Is there a pipeline to obtain required input annotation files for any other genomes? For example, I have rice genome sequences in fasta and annotations in gff format, how to prepare the requir…
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Hello, I apologize for the novice question but I am trying to run TAMA Collapse and then TAMA Merge on isoseq data that has been mapped to a genome, once using minimap2 and once using uLTRA with a pre…
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Add nf-core module to both ``genome`` only and ``genome_and_annotation`` subworkflows.
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Thank you so much for your tool! I have genome files and annotation GFF files for two species, and I mainly want to use TOGA to identify orthologs between them. However, when I run it, the gene IDs an…
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This issue documents the progress in #148:
- Converted the trie-building algorithm to C++, including C++ versions of the two involved classes (`TrieInnerNode` and `TrieLeafNode`). This performs the…