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Alignments Tutorial #29

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Alignments Tutorial #29

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c017a7d
add rough draft alignments
danielle-pinto Mar 9, 2026
33dfbd4
finish draft of BioAlignments package explanation
danielle-pinto Mar 10, 2026
d3892a3
rebase onto main and make edits according to kevin's review
danielle-pinto Mar 12, 2026
adc2a1d
add example to compare mecA vs mecA1
danielle-pinto Mar 13, 2026
d20b9bd
fix grammar and typos
danielle-pinto Mar 15, 2026
756269a
add slight edit about MSAs and mapping
danielle-pinto Mar 15, 2026
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5 changes: 2 additions & 3 deletions cookbook/sequences.md → cookbook/01-sequences.md
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Expand Up @@ -228,8 +228,7 @@ meaning the majority of reads are high quality.

More information about converting ASCII characters and PHRED scores to quality scores can be found [here](https://people.duke.edu/~ccc14/duke-hts-2018/bioinformatics/quality_scores.html).

Now that we've learned how to read files in and manipulate them a bit,
let's see if we can align the _mecA_ gene to the _Staphylococcus aureus_ genome.
This will tell us if this particular _S. aureus_ is MRSA.
Now that we've learned how to read files in and manipulate them a bit,
let's see if we can align 2 _mecA_ genes to compare them.


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