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Hi,
I was really impressed with the pipeline you developed and would like to use it for my own work. I managed to install the pipeline and run the test, however with my own data it has proven itse…
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When I tired to use CreateModelEggNogPool.carveme_pipeline("Scer", "Saccharomyces_cerevisiae_S288C_GCF_000146045.2","data/annotations/functional/example.fasta.emapper.annotations","data/annotations/fa…
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### Description of feature
One of the issues that repeatedly causes confusion amongst users of the rnaseq pipeline is the reference transcriptome annotation to be provided as GTF or GFF3 (_which is…
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TL;DR - there are uniprot KW and EC annotations to this family that contradict the literature.
I'll take yeast RAD26 as an exemplar here, but similar patterns are seen in orthologs.
Uniprot has …
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Hello,
I have been working with scGPT for the last week and I am studying currently the GRN part. By running the Tutorial_GRN notebook, and downloading the data/model in the links provided, I am un…
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Alex has create a test file containing all human annotations that GO Central want to load:
> The set of protein accessions included in this file is based on UniProt reference proteomes, which provide…
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Hi Brian,
I am using PASA to annotate a genome assembly following the PASA tutorial. The genome is ~500 MB and resulted in 400 contigs. EVM ran successfully and outputted 33k genes (with evidence f…
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Hi~
I used the hisat2-stringtie pipeline to deal with RNA-seq data and got a result with MSTRG tags. Some of them had gene name which was convenient to do function annotation after. But 1/3 of my dat…
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### Description of the bug
Hello,
I am having trouble with the sample input file. I have .csv file with correct file names and format as described in the pipeline page (also attached here). I get …
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Is there a way to adapt the pipeline for nonhuman organisms?