User: jubillante

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jubillante0
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Posts by jubillante

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Answer: A: Getting taxonomy information from PFAM
... Here is how I got taxonomy strings starting with a fasta seed alignment 1. Get the list of accession IDs ``` grep ">" seed.fasta | sed 's/>//' |cut -f1 -d'/' > pfamaccessioncodes.txt ``` 2. Upload your list (or copy and paste) into the Retrieve/ID mapping tool https://www.uniprot.org/uplo ...
written 10 weeks ago by jubillante0
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Answer: A: How to get pfam seed sequence taxonomy info?
... Here is how I got taxonomy strings starting with a fasta seed alignment 1. Get the list of accession IDs ``` grep ">" seed.fasta | sed 's/>//' |cut -f1 -d'/' > pfamaccessioncodes.txt ``` 2. Upload your list (or copy and paste) into the Retrieve/ID mapping tool https://www.uniprot.org/uplo ...
written 10 weeks ago by jubillante0
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Comment: C: Taxonomic assignment of bins found by Maxbin2
... This is a late reply but for anyone wondering how to fix this use the option -f to redirect the stdout (with taxonomy table and stats) to a file: checkm lineage_wf bins outputfolder -f output.txt ...
written 11 months ago by jubillante0

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