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DerKevinRiehl / transposon_annotation_reasonaTE

Transposon annotation tool "resonaTE" (part of TransposonUltimate)
GNU General Public License v3.0
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pipeline issue #17

Open zuodabin opened 1 year ago

zuodabin commented 1 year ago

Hi DerKevinRiehl~ Now I want to annotate the TE of the genome, but I don't know which step or pipeline to start with. Could you please send me an annotation process? Thank you!

DerKevinRiehl commented 1 year ago

Dear Zuodabin,

as you can find in the tutorial section "how to use reasonate" https://github.com/DerKevinRiehl/transposon_annotation_reasonaTE#how-to-use-reasonate you need to do following steps to annotate your genome:

Step 1) Create a project

conda activate transposon_annotation_tools_env
mkdir workspace
wget https://raw.githubusercontent.com/DerKevinRiehl/transposon_annotation_reasonaTE/main/workspace/testProject/sequence.fasta # demo fasta you could use
reasonaTE -mode createProject -projectFolder workspace -projectName testProject -inputFasta sequence.fasta

Step 2) Annotate genome with annotation tools To annotate the genome with different annotation tools, four possible ways exist. We recommend Option 2 as it allows for parallelization which is vital for reducing processing times for very large genomes.

conda activate transposon_annotation_tools_env
reasonaTE -mode annotate -projectFolder workspace -projectName testProject -tool all

Step 3) Parse annotations Each of the tools will produce different output file formats. reasonaTE therefore provides a parser module that will unify different output files to one standardized format (GFF3). The parser module will automatically detect annotations that are available as a result from step 2, and only the available files will be considered in the next steps by the pipeline.

conda activate transposon_annotation_tools_env
reasonaTE -mode parseAnnotations -projectFolder workspace -projectName testProject

Step 4) Run the pipeline on the genome annotations

conda activate transposon_annotation_reasonaTE
reasonaTE -mode pipeline -projectFolder workspace -projectName testProject

Step 5) Calculate final statistics Once all results are calculated, summarizing statistics can be generated using:

conda activate transposon_annotation_reasonaTE
reasonaTE -mode statistics -projectFolder workspace -projectName testProject

Hope this could help a little, please let me know if you have further questions and if this helped you.

Best, Kevin Riehl