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sofstam 2023-02-17 13:43:38 +01:00
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docs/output.md
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@ -449,15 +449,15 @@ The resulting HTML files can be loaded into your web browser for exploration. Ea
The following report files are used for the taxpasta step:
- Bracken: `<sample>_<db_name>.tsv`
- Centrifuge: `<sample_id>.centrifuge.txt`
- Diamond: `<sample_id>`
- Kaiju: `<sample_id>_<db_name>.kaijutable.txt`
- KrakenUniq: `<sample_id>_<db_name>.report.txt`
- Kraken2: `<sample_id>_<db_name>.report.txt`
- MALT: `<sample_id>.txt.gz`
- MetaPhlAn3: `<sample_id>_profile.txt`
- mOTUs: `<sample_id>.out`
- Bracken: `<sample>_<db_name>.tsv` Taxpasta used the `new_est_reads` column for the standardised profile.
- Centrifuge: `<sample_id>.centrifuge.txt` Taxpasta uses the `direct_assigned_reads` column for the standardised profile.
- Diamond: `<sample_id>` Taxpasta summarises number of reads per NCBI taxonomy ID standardised profile.
- Kaiju: `<sample_id>_<db_name>.kaijutable.txt` Taxpasta uses the `reads` column from kaiju2table standardised profile.
- KrakenUniq: `<sample_id>_<db_name>.report.txt` Taxpasta uses the `reads` column for the standardised profile.
- Kraken2: `<sample_id>_<db_name>.report.txt` Taxpasta uses the `direct_assigned_reads` column for the standardised profile.
- MALT: `<sample_id>.txt.gz` Taxpasta uses the `count` (second) column from the output of MEGAN6's rma2info for the standardised profile.
- MetaPhlAn3: `<sample_id>_profile.txt` Taxpasta uses the `relative_abundance` column multiplied with a fixed number to yield an integer for the standardised profile.
- mOTUs: `<sample_id>.out` Taxpasta uses the `read_count` column for the standardised profile.
### MultiQC