From ff4324ebbf943feee4095eaa3aa1e36a5d9fe4c0 Mon Sep 17 00:00:00 2001 From: jianhong Date: Mon, 19 Feb 2024 13:49:25 +0000 Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20jianhong?= =?UTF-8?q?/genomictools@39e07579e5965410444c571085952af5735dd657=20?= =?UTF-8?q?=F0=9F=9A=80?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- articles/scripts.html | 10 +++++----- pkgdown.yml | 2 +- 2 files changed, 6 insertions(+), 6 deletions(-) diff --git a/articles/scripts.html b/articles/scripts.html index 3616886..91de058 100644 --- a/articles/scripts.html +++ b/articles/scripts.html @@ -132,13 +132,13 @@

Install dockerYou may want to open the source of “scripts.Rmd” at the “Source Panes” by

-rstudioapi::documentOpen("/usr/local/lib/R/site-library/basicBioinformaticsDRC2023/doc/scripts.Rmd")
+rstudioapi::documentOpen("/usr/local/lib/R/site-library/basicBioinformaticsDRC2024/doc/scripts.Rmd")

Run kallisto and Salmon for RNA-seq

-

The sample files are packaged in basicBioinformaticsDRC2023 package +

The sample files are packaged in basicBioinformaticsDRC2024 package and Docker container.

Now we will download the zebrafish cDNA files from ENSEMBL in order to build the Kallisto and Salmon transcript index. If you are doing rRNA @@ -157,7 +157,7 @@

Run kallisto and Salmon for RNA-seq 
mkdir data/RNAseq
 cd data/RNAseq
 # wget https://raw.githubusercontent.com/jianhong/genomictools/master/inst/extdata/Danio_rerio.GRCz11.cdna.toy.fa.gz
-ln -s /usr/local/lib/R/site-library/basicBioinformaticsDRC2023/extdata/Danio_rerio.GRCz11.cdna.toy.fa.gz ./
+ln -s /usr/local/lib/R/site-library/basicBioinformaticsDRC2024/extdata/Danio_rerio.GRCz11.cdna.toy.fa.gz ./

It will take several seconds to build the toy index.

kallisto index -i danRer.GRCz11_transcrits.toy.idx Danio_rerio.GRCz11.cdna.toy.fa.gz
 
@@ -228,7 +228,7 @@ 
prepare the transcripts to g
 the pre-saved object for the toy data.

 
 # t2g <- readRDS(url("https://raw.githubusercontent.com/jianhong/genomictools/master/inst/extdata/t2g.rds"))
-t2g <- readRDS(system.file("extdata", "t2g.rds", package = "basicBioinformaticsDRC2023"))
+t2g <- readRDS(system.file("extdata", "t2g.rds", package = "basicBioinformaticsDRC2024"))
 head(t2g, n=3)

 
The following codes are using tximport to import the transcripts
 counts and aggregate to gene level. Downstream are using DESeq2 to do
@@ -325,7 +325,7 @@ 
prepare index file for bwaThe data are only a subset of the whole genome. We will only use
 genes in chromosome 4, 13, 16 and 21 to speed up the test run.

 
# wget https://raw.githubusercontent.com/jianhong/genomictools/master/inst/extdata/Danio_rerio.GRCz11.dna.toy.fa.gz
-ln -s /usr/local/lib/R/site-library/basicBioinformaticsDRC2023/extdata/Danio_rerio.GRCz11.dna.toy.fa.gz ./
+ln -s /usr/local/lib/R/site-library/basicBioinformaticsDRC2024/extdata/Danio_rerio.GRCz11.dna.toy.fa.gz ./
 ## the following step will take about 3min
 bwa index -p GRCz11.toy Danio_rerio.GRCz11.dna.toy.fa.gz
diff --git a/pkgdown.yml b/pkgdown.yml index 715494a..e2328ba 100644 --- a/pkgdown.yml +++ b/pkgdown.yml @@ -3,7 +3,7 @@ pkgdown: 2.0.7 pkgdown_sha: ~ articles: scripts: scripts.html -last_built: 2024-02-19T13:43Z +last_built: 2024-02-19T13:49Z urls: reference: https://jianhong.github.io/genoimctools/reference article: https://jianhong.github.io/genoimctools/articles