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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 ## <a name="map-reads"></a>Mapping Genomic Reads
* Map example E. coli PacBio reads (takes about 12 wall-clock seconds): ### Map PacBio reads
```sh ```sh
minimap2 -ax map-pb -t4 ecoli_ref.fa ecoli_p6_25x_canu.fa > mapped.sam 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 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.* line. *Please always make sure you are using an intended pre-built index.*
* Map Illumina paired-end reads: ### Map Illumina paired-end reads:
```sh ```sh
minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq > mapped-sr.sam 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 ```sh
minimap2 -ax sr ecoli_ref.fa ecoli_mason_1.fq ecoli_mason_2.fq | paftools.js mapeval - 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 3. Number of wrong mappings in the same mapQ interval
4. Accumulative mapping error rate 4. Accumulative mapping error rate
5. Accumulative number of mappings 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).