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Hello,
I have previously used your tool on 16S, and it was truly fascinating. Currently, I am working with ITS and would like to incorporate picrust2 into my analysis.
I have already reviewed the FAQ section related to this topic
, but I am still struggling to understand the specific changes I need to make.
Currently, I am running picrust2_pipeline.py directly for 16S with the following command: (picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1
) .
For ITS, I believe I need to modify the command to generate EC_metagenome_out
I think I need to add the following options to the previous command line: --custom_trait_tables, --marker_gene_table, and --reaction_func. However, I'm uncertain about what to replace XXXXX with in each case:
Yes, it looks like you've got that correctly for running PICRUSt2 with ITS. I'm afraid that there isn't currently a file that maps the fungal genomes to KO's as there is for 16S.
Hello,
I have previously used your tool on 16S, and it was truly fascinating. Currently, I am working with ITS and would like to incorporate picrust2 into my analysis.
I have already reviewed the FAQ section related to this topic
, but I am still struggling to understand the specific changes I need to make.
Currently, I am running picrust2_pipeline.py directly for 16S with the following command: (picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1
) .
For ITS, I believe I need to modify the command to generate EC_metagenome_out
I think I need to add the following options to the previous command line: --custom_trait_tables, --marker_gene_table, and --reaction_func. However, I'm uncertain about what to replace XXXXX with in each case:
picrust2_pipeline.py -s study_seqs.fna -i study_seqs.biom -o picrust2_out_pipeline -p 1 --custom_trait_tables XXXXXXX --marker_gene_table XXXXX --reaction_func XXXX
and maybe adding this -r picrust2/picrust2/default_files/fungi/fungi_ITS ?
I tried this command based on this post #101 but I don't know if it's correct or not
picrust2_pipeline.py -s /lab/user/data/ubiome_local_test/picrust_ITS_mock_input/ASV-sequences.fasta -i /lab/user/data/ubiome_local_test/picrust_ITS_mock_input/feature-table.biom -o picrust2_out_pipeline -p 4 --custom_trait_tables /opt/conda/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/fungi/ec_ITS_counts.txt.gz --min_reads 1 -r /opt/conda/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/fungi/fungi_ITS --marker_gene_table /opt/conda/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/fungi/ITS_counts.txt.gz --pathway_map /opt/conda/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/pathway_mapfiles/metacyc_path2rxn_struc_filt_fungi_present.txt --reaction_func /opt/conda/envs/picrust2/lib/python3.8/site-packages/picrust2/default_files/fungi/ec_ITS_counts.txt.gz
-Is there a way to generate KO_metagenome_out file as it's the case for 16s ?
![image](https://private-user-images.githubusercontent.com/149370431/291336735-f2fa94fc-2c13-48d2-9b1b-8c1fc246e2c5.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MjE1MjExNjksIm5iZiI6MTcyMTUyMDg2OSwicGF0aCI6Ii8xNDkzNzA0MzEvMjkxMzM2NzM1LWYyZmE5NGZjLTJjMTMtNDhkMi05YjFiLThjMWZjMjQ2ZTJjNS5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwNzIxJTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDcyMVQwMDE0MjlaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT01ZjZjOGQ4YWI3M2IyYmM5MWNmY2ExYTdjNjczMDgwMGFkZWNmOWYyZDZhZDg5Y2U3MDE2YmQ1MWQ2ZGIzYzdlJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.XlGgxVSOTuBUKTnrFmTSHVsbnQ_zyhUOtCnZRT1JnTc)
I really hope that someone can help me with this :)
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