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Pull request overview
Adds documentation for running a new PHROGs annotation/counting step as part of the pawsey_shortread workflow, and adjusts README section formatting to include it in the numbered pipeline.
Changes:
- Promotes step 2 into a proper Markdown heading.
- Introduces a new “PHROGs” section with example Slurm submissions (and renumbers subsequent sections).
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| # 2. Check the names of your files. | ||
| ## 2. Check the names of your files. |
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| We can use the mmseqs analysis to find PHROGs. We have a mapping between the UniProt IDs and the PHOG IDs which we use to map | ||
| similarities. |
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| PHROGJOB=$(sbatch --parsable --dependency=afterok:$MMSEQSJOB --array=1-$NUM_R1_READS:1 $PAWSEY_SRC/mmseqs_add_phrog_function.slurm) | ||
| sbatch --parsable --dependency=afterok:$PHROGJOB $PAWSEY_SRC/count_phrog_functions.slurm |
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