updated cookbook

cookbook.md

@@ -6,16 +6,50 @@
 ## <a name="install"></a>Installation
 
 ```sh
+# install minimap2 executables
 curl -L https://github.com/lh3/minimap2/releases/download/v2.9/minimap2-2.9_x64-linux.tar.bz2 | tar jxf -
-export PATH="$PATH:"`pwd`                              # set up PATH
 cp minimap2-2.9_x64-linux/{minimap2,k8,paftools.js} .  # copy executables
-cp minimap2-2.9_x64-linux/test/MT-*.fa .               # copy small examples
-curl -L https://github.com/lh3/minimap2/releases/download/v2.0/ecoli.tgz | tar zxf -
+export PATH="$PATH:"`pwd`                              # put the current directory on PATH
+# download example datasets
+curl -L https://github.com/lh3/minimap2/releases/download/v2.0/cookbook-data.tgz | tar zxf -
 ```
 
 ## <a name="map-reads"></a>Mapping Genomic Reads
 
-* Map example E. coli reads (takes about 12 wall-clock seconds):
+* Map example E. coli PacBio reads (takes about 12 wall-clock seconds):
   ```sh
   minimap2 -ax map-pb -t4 ecoli_ref.fa ecoli_p6_25x_canu.fa > mapped.sam
   ```
+  Alternatively, you can create a minimap2 index first and then map:
+  ```sh
+  minimap2 -x map-pb -d ecoli-pb.mmi ecoli_ref.fa                      # create an index
+  minimap2 -ax map-pb ecoli-pb.mmi ecoli_p6_25x_canu.fa > mapped.sam
+  ```
+  This will save you a couple of minutes when you map against the human genome.
+  **HOWEVER**, key algorithm parameters such as the k-mer length and window
+  size can't be changed after indexing. Minimap2 will give you a warning if
+  parameters used in a pre-built index doesn't match parameters on the command
+  line. *Please always make sure you are using an intended pre-built index.*
+
+* Map Illumina paired-end reads:
+  ```sh
+  minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq > mapped-sr.sam
+  ```
+
+* Evaluating mapping accuracy with simulated reads:
+  ```sh
+  minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq | paftools.js mapeval -
+  ```
+  The output is:
+  ```
+  Q       60      19712   0       0.000000000     19712
+  Q       0       282     219     0.010953286     19994
+  U       6
+  ```
+  where a line starting with `Q` gives:
+  1. Mapping quality (mapQ) threshold
+  2. Number of mapped reads between this threshold and the previous mapQ threshold.
+  3. Number of wrong mappings in the same mapQ interval
+  4. Accumulative mapping error rate
+  5. Accumulative number of mappings
+  A `U` line gives the number of unmapped reads (for SAM input only)