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miRTop / mirtop

command lines tool to annotate miRNAs with a standard mirna/isomir naming
https://mirtop.readthedocs.org
MIT License
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How can I get files like tagMir-all.gff? #57

Open illumination-k opened 4 years ago

illumination-k commented 4 years ago

Hi, I would like to analyze isomiRs by using isomiR-SEA ,mirtop and R-package(isomiRs).

Your quick start example to import isomiR-SEA files is (and maybe your example of 'isomiR-SEA' is example of 'validation')


mirtop gff --format isomirsea -sps hsa --hairpin  examples/annotate/hairpin.fa --gtf  examples/annotate/hsa.gff3 -o  test_out examples/isomir-sea/tagMir-all.gff

But I think isomiR-SEA generate just below files... • out_result_mature_21_ambigue.txt • out_result_mature_21_ambigue_ambigue_selected.txt • out_result_mature_21_tag_ambigue.txt • out_result_mature_21_tag_ambigue_selected.txt • out_result_mature_21_tag_unique.txt • out_result_mature_21_unique.txt • out_result_mature_21_unique_ambigue_selected.txt

So I wondered how can I get files like tagMir-all.gff.

Can you tell me how can I generate this?

lpantano commented 4 years ago

Thank very much for the question, I will tag @gurgese who is the developer of isomir-sea. I will add that to the documentation when we get the answer from him.

Thanks!