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cdanielmachado / carveme_paper

Data and scripts for the paper "Fast automated reconstruction of genome-scale metabolic models for microbial species and communities"
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tsv output #2

Closed Avitzm closed 3 years ago

Avitzm commented 3 years ago

Can you please provide the column titles of the tsv ouput file? Thanks!

cdanielmachado commented 3 years ago

Hi, the output TSV file comes from DIAMOND, you can find in their documentation more details about the columns:

https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options

In particular:

"By default, there are 12 preconfigured fields: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore."

Avitzm commented 3 years ago

Could you please also explain the xml file or tell me where to find a full description of it? Thanks

From: Daniel Machado @.> Sent: Tuesday, April 6, 2021 2:12 PM To: cdanielmachado/carveme_paper @.> Cc: Michal Avitzour @.>; Author @.> Subject: Re: [cdanielmachado/carveme_paper] tsv output (#2)

Hi, the output TSV file comes from DIAMOND, you can find in their documentation more details about the columns:

https://github.com/bbuchfink/diamond/wiki/3.-Command-line-options

In particular:

"By default, there are 12 preconfigured fields: qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore."

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cdanielmachado commented 3 years ago

Sure, the models are in SBML format: http://sbml.org/Main_Page