From ad1beaf255f4ae474c4bb3c5d2714de1d7086f10 Mon Sep 17 00:00:00 2001 From: Heng Li Date: Mon, 12 Mar 2018 13:20:25 -0400 Subject: [PATCH] backup; not finished --- cookbook.md | 22 +++++++++++++++++++--- 1 file changed, 19 insertions(+), 3 deletions(-) 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