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bobeobibo / phigaro

Phigaro is a scalable command-line tool for predicting phages and prophages
MIT License
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issues about output Files #46

Closed qianxin-kxy closed 8 months ago

qianxin-kxy commented 1 year ago

This is a very interesting and useful tool, but I have a question, which is the bed file in the output results, some of which have the following display (phigaro) [kxy@zju Phigaro]$ cd /data/users/kxy/kxytry/assembleddata/analysis/phage/Phigaro/sp_2017_ST195_67074 (phigaro) [kxy@zju sp_2017_ST195_67074]$ more sp_2017_ST195_67074.phigaro.bed

gff-version 3.2.1

NODE_34_length_35751_cov_67.7224 4909 9641 prophage1 . . NODE_34_length_35751_cov_67.7224 15713 31032 prophage2 . . NODE_34_length_35751_cov_67.7224 4909 5353 gene10 3.6e-84 - NODE_34_length_35751_cov_67.7224 5546 5789 gene11 . + NODE_34_length_35751_cov_67.7224 5795 5999 gene12 . - NODE_34_length_35751_cov_67.7224 6137 6641 gene13 . - NODE_34_length_35751_cov_67.7224 6642 7650 gene14 3.2e-194 - NODE_34_length_35751_cov_67.7224 7701 7917 gene15 9.2e-52 - NODE_34_length_35751_cov_67.7224 7931 8684 gene16 . - NODE_34_length_35751_cov_67.7224 8987 9308 gene17 . + NODE_34_length_35751_cov_67.7224 9369 9642 gene18 5.1e-54 + NODE_34_length_35751_cov_67.7224 15713 16058 gene30 . + NODE_34_length_35751_cov_67.7224 16266 16503 gene31 0.017 + NODE_34_length_35751_cov_67.7224 17167 17623 gene32 . + NODE_34_length_35751_cov_67.7224 17683 18118 gene33 7.3e-84 +

I want to know if there are no specific names for prophage1 and prophage2? Or is it a newly discovered prophage? Because I have hundreds of genomes to process and have already processed them, but I have to group them for statistics in the future. I don't know how to treat the prophages in the bed files corresponding to each genome。

In addition, are the following genes 10, 11, etc. bacteriophages or other special mobile components

PollyTikhonova commented 8 months ago

In version 2.4.0 I added taxonomy information about taxonomy to gff3 format. Also, this information was in .tsv and .htmlfiles of previous version of phigaro. We can't say for sure what are those genes, in .tsvand .htmlfiles you can see the lists of pvogs, for those genes that were matched. For some of those there are functions prediction (they are demonstrated in .html)