From 0173850ef009b88930753a5451b2d05698fa05e3 Mon Sep 17 00:00:00 2001
From: Heng Li <lh3@me.com>
Date: Mon, 12 Mar 2018 12:42:13 -0400
Subject: [PATCH] don't use bullets - they are hard to read

---
 cookbook.md | 70 ++++++++++++++++++++++++++---------------------------
 1 file changed, 35 insertions(+), 35 deletions(-)

diff --git a/cookbook.md b/cookbook.md
index 4e766e6..9a21d25 100644
--- a/cookbook.md
+++ b/cookbook.md
@@ -16,40 +16,40 @@ curl -L https://github.com/lh3/minimap2/releases/download/v2.0/cookbook-data.tgz
 
 ## <a name="map-reads"></a>Mapping Genomic Reads
 
-* 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 PacBio reads
+```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
-  ```
+### 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)
+### 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).