lecture_notes:05-29-2015
Differences
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lecture_notes:05-29-2015 [2015/05/29 18:30] chkan created |
lecture_notes:05-29-2015 [2015/05/29 18:37] (current) chkan Added figures |
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| Basic Kmer Counting | Basic Kmer Counting | ||
| - | - Naïve python way [insert picture] | + | - Naïve python way (See Figure 1) |
| ○ Okay if you're in a microbial genome | ○ Okay if you're in a microbial genome | ||
| ○ Runs out of memory | ○ Runs out of memory | ||
| Line 14: | Line 14: | ||
| ○ Process Kmers one character at a time to avoid building big strings | ○ Process Kmers one character at a time to avoid building big strings | ||
| § Look at sequences a kmer at a time | § Look at sequences a kmer at a time | ||
| - | ○ How to compress results | + | ○ How to compress results (See Figure 2) |
| § Strings are inefficient way to store kmers | § Strings are inefficient way to store kmers | ||
| § Want to compress keys and values | § Want to compress keys and values | ||
| Line 60: | Line 60: | ||
| </code> | </code> | ||
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| + | Figure 1 | ||
| + | {{:lecture_notes:lecture051915_fig1.jpg?400|}} | ||
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| + | ---- | ||
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| + | Figure 2 | ||
| + | {{:lecture_notes:lecture051915_fig2.jpg?200|}} | ||
lecture_notes/05-29-2015.1432924233.txt.gz · Last modified: 2015/05/29 18:30 by chkan
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