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don't use bullets - they are hard to read

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Heng Li 2018-03-12 12:42:13 -04:00
parent acea3594fb
commit 0173850ef0
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cookbook.md
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@ -16,7 +16,7 @@ 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):
### Map PacBio reads
```sh
minimap2 -ax map-pb -t4 ecoli_ref.fa ecoli_p6_25x_canu.fa > mapped.sam
```
@ -31,12 +31,12 @@ curl -L https://github.com/lh3/minimap2/releases/download/v2.0/cookbook-data.tgz
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:
### 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:
### Evaluating mapping accuracy with simulated reads:
```sh
minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq | paftools.js mapeval -
```
@ -52,4 +52,4 @@ curl -L https://github.com/lh3/minimap2/releases/download/v2.0/cookbook-data.tgz
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)
A `U` line gives the number of unmapped reads (for SAM input only).