From 75fea7e572ec7f83df0fa8912e3e45e9dd4b40a0 Mon Sep 17 00:00:00 2001 From: jessicamizzi Date: Tue, 23 Oct 2018 13:42:19 -0700 Subject: [PATCH 1/5] Rename 00a-background.md to 01-background.md --- _episodes/{00a-background.md => 01-background.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename _episodes/{00a-background.md => 01-background.md} (100%) diff --git a/_episodes/00a-background.md b/_episodes/01-background.md similarity index 100% rename from _episodes/00a-background.md rename to _episodes/01-background.md From 66c9100a8a4b7055e5a199f87697ad3e53ad77c6 Mon Sep 17 00:00:00 2001 From: jessicamizzi Date: Tue, 23 Oct 2018 13:42:58 -0700 Subject: [PATCH 2/5] Rename 00-quality-control.md to 02-quality-control.md --- _episodes/{00-quality-control.md => 02-quality-control.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename _episodes/{00-quality-control.md => 02-quality-control.md} (100%) diff --git a/_episodes/00-quality-control.md b/_episodes/02-quality-control.md similarity index 100% rename from _episodes/00-quality-control.md rename to _episodes/02-quality-control.md From 34162639bd96a36c0984b51b733a527fbf0698b8 Mon Sep 17 00:00:00 2001 From: jessicamizzi Date: Tue, 23 Oct 2018 13:43:24 -0700 Subject: [PATCH 3/5] Rename 01-trimming.md to 03-trimming.md --- _episodes/{01-trimming.md => 03-trimming.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename _episodes/{01-trimming.md => 03-trimming.md} (100%) diff --git a/_episodes/01-trimming.md b/_episodes/03-trimming.md similarity index 100% rename from _episodes/01-trimming.md rename to _episodes/03-trimming.md From 2afbb69e2bcd1e3ad6770b07a062e79476dbb7eb Mon Sep 17 00:00:00 2001 From: jessicamizzi Date: Tue, 23 Oct 2018 13:43:42 -0700 Subject: [PATCH 4/5] Rename 03-automation.md to 04-automation.md --- _episodes/{03-automation.md => 04-automation.md} | 0 1 file changed, 0 insertions(+), 0 deletions(-) rename _episodes/{03-automation.md => 04-automation.md} (100%) diff --git a/_episodes/03-automation.md b/_episodes/04-automation.md similarity index 100% rename from _episodes/03-automation.md rename to _episodes/04-automation.md From 1c177fe8f44c266bf356e4e1b89c89f926476c74 Mon Sep 17 00:00:00 2001 From: jessicamizzi Date: Tue, 23 Oct 2018 13:46:30 -0700 Subject: [PATCH 5/5] update names of episodes --- _extras/guide.md | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/_extras/guide.md b/_extras/guide.md index b0b26402..c3dcf9ae 100644 --- a/_extras/guide.md +++ b/_extras/guide.md @@ -1,4 +1,4 @@ ---- + --- layout: page title: "Instructor Notes" permalink: /guide/ @@ -9,7 +9,7 @@ permalink: /guide/ This lesson currently uses the `open` command to view FastQC output on its local browser. The `open` command is great for Macs, but there is currently no command listed in the lesson that works for Macs. The `explore` command may be useful here. If a solution is found, it's worth adding to the lesson. ## SAMtools or IGV? -Some instructors chose to use SAMtools tview for visualization of variant calling results while other prefer than IGV. SAMtools is the default because installation of IGV can take up additional instruction time, and SAMtools tview is sufficient to visualize results. However, episode 02-variant_calling includes instructions for installation and using IGV. +Some instructors chose to use SAMtools tview for visualization of variant calling results while other prefer than IGV. SAMtools is the default because installation of IGV can take up additional instruction time, and SAMtools tview is sufficient to visualize results. However, episode 04-variant_calling includes instructions for installation and using IGV. ## Commands with Lengthy Run Times @@ -106,7 +106,7 @@ $ bwa mem data/ref_genome/ecoli_rel606.fasta data/trimmed_fastq_small/SRR2584866 ~~~ #### The Automation Episode -The code blocks at the beginning of the automation episode (03-automation.md) are examples of for loops and scripts and are not meant to be run by learners. The first code chunks that should be run are under Analyzing Quality with FastQC. +The code blocks at the beginning of the automation episode (05-automation.md) are examples of for loops and scripts and are not meant to be run by learners. The first code chunks that should be run are under Analyzing Quality with FastQC. Also, after the first code chunk of code meant to be run, there is a line that reads only `read_qc.sh` and will yield a message saying that this command wasn't found. After the creation of the script, this command will run the script that will be written.