TOGA
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hillerlab
TOGA (Tool to infer Orthologs from Genome Alignments): implements a novel paradigm to infer orthologous genes. TOGA integrates gene annotation, inferring orthologs and classifying genes as intact or l...
Hello, dev team! I'm very new to TOGA, and I'm trying it out on some public data for a class project. When I run it on my personal Windows machine...
High I am running, when I run in my data I got the error "Could not split CESAR jobs". I run the following line: ./toga.py make_lastz_chains/make_lastz_chains/chicken_turkey/target.query.final.chain.gz ../chicken/genes.bed12 ../chicken/galGal6.2bit ../turkey/melGal5.2bit --pn...
Simply replacing `U12 exons` with `U12 introns` (correct me if this is not a typo) in README.md
Nextflow creates quite a sophisticated structure of folders, files, and hidden files, where it stores the run information. Need to find, or implement a module (maybe a separate library?) to...
Hi, I am wondering whether TOGA can also be used to estimate gene age (when different genes appeared in the tree). I know gene_age-dating pipeline (https://github.com/Zhanglab-IOZ/SBP_age-dating/blob/master/pipeline.md) from Zhang lab. uses...
Hi, authors I have successfully completed the TOGA process for several species. I wanted to focus on the differences between species, so I screened the "L" gene sets and analyzed...
Hi Recently, I've been using annotation files for some species obtained via the TOGA method from Zoonomia. When I attempted to extract CDS and PEP from these annotation files and...
Hello! Thank you for this fantastic annotation tool. I was hoping to use TOGA to annotate my rodent but using a more closely related reference species than mmus, as I...
Hello,Professor I downloaded the TOGA result file for several species from https://genome.senckenberg.de/download/TOGA/mouse_mm10_reference/Rodentia/. I focused on a gene ENSMUSG00000057170 and the gene is showed loss status in the loss_summ_data.tsv file. The...
I perform a wide-scale test using the recommonded scripts " ./toga.py test_input/hg38.mm10.chr11.chain test_input/hg38.genCode27.chr11.bed test_input/hg38.2bit test_input/mm10.2bit --kt --pn test -i supply/hg38.wgEncodeGencodeCompV34.isoforms.txt --nc ./nextflow_config_files --cb 3,5 --cjn 500 --u12 supply/hg38.U12sites.tsv --ms", But...
