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Update admonitions
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JSBoey committed Sep 4, 2024
1 parent ae77e24 commit 926dafe
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16 changes: 9 additions & 7 deletions docs/day2/ex9_refining_bins.md
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Expand Up @@ -417,14 +417,16 @@ Then, we use SeqKit to extract the required contigs.

If you want to use the `vb_omit_contigs_tmp.txt` as the search pattern to omit contigs from the bins, you can do that following:

```bash
module purge
module load SeqKit/2.4.0
!!! terminal "code"

for bins in mock_bins/*.fna; do
seqkit grep -v -f vb_omit_contigs.tmp.txt > refined_bins/$(basename ${bins} .fna).refined.fna
done
```
```bash
module purge
module load SeqKit/2.4.0

for bins in mock_bins/*.fna; do
seqkit grep -v -f vb_omit_contigs.tmp.txt > refined_bins/$(basename ${bins} .fna).refined.fna
done
```

In the code above, we added a `-v` to the `grep` command to indicate invert matches.

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