diff --git a/cookbook.md b/cookbook.md
index 8b4d99f..3e8fca1 100644
--- a/cookbook.md
+++ b/cookbook.md
@@ -7,7 +7,7 @@
* [Evaluating mapping accuracy with simulated reads (for developers)](#mapeval)
- [Read Overlap](#read-overlap)
* [Long-read overlap](#long-read-overlap)
- * [Evaluating overlap sensitivity](#ov-eval)
+ * [Evaluating overlap sensitivity (for developers)](#ov-eval)
## Installation
@@ -76,6 +76,8 @@ paftools.js mason2fq tmp.sam | seqtk seq -1 > ecoli_mason_1.fq
paftools.js mason2fq tmp.sam | seqtk seq -1 > ecoli_mason_2.fq
```
+
+
## Read Overlap
### Long read overlap
@@ -89,9 +91,9 @@ Here we explicitly applied `-r 10000`. We are considering to set this as the
default for the `ava-ont` mode as this seems to improve the contiguity for
nanopore read assembly (Loman, personal communication).
-**Minimap2 doesn't work well with short-read overlap.**
+*Minimap2 doesn't work well with short-read overlap.*
-### Evaluating overlap sensitivity
+### Evaluating overlap sensitivity (for developers)
```sh
# read to reference mapping
@@ -102,5 +104,19 @@ sort -k6,6 -k8,8n to-ref.paf | paftools.js ov-eval - overlap.paf
You can see that for PacBio reads, minimap2 achieves higher overlap sensitivity
with `-x ava-pb` (99% vs 93% with `-x ava-ont`).
+
+
+## Mapping Long RNA-seq Reads
+
+(Unfinished section. Data to come later...)
+
+### Mapping Nanopore direct-RNA reads
+
+```sh
+minimap2 -ax splice -k14 -uf ref.fa reads.fa > aln.sam
+```
+
+
+
[pbsim]: https://github.com/pfaucon/PBSIM-PacBio-Simulator
[mason2]: https://github.com/seqan/seqan/tree/master/apps/mason2