Step 1, I need to create a repository on my github central place

	
Create a new repository called 'rShiny' at github
	
git clone https://github.com/2waybene/rShiny rShiny under "myGit"
	
I have an account with basic feature at shinyapps
	
This one was for Dr. Cui, his project on MotionDetection

Step 2 RShiny tutorial

	
Here is the main tutorial page from RStudio
	
And, there are many examples in this gallery.

Some special RShiny note

	
Install shinyIncubator needs devtools

To start shinyapp on the command line, use the following command

R --vanilla -e "shiny::runApp('.', port=8888, host='10.91.128.1')"
R --vanilla -e "shiny::runApp('.', port=8888, host='localhost')"

Then go to a browser to load the application. For some reason, it fails to work with the follow error message

Arraystar provides services

It turns out that sra toolkit is not very straightforward, it deserves the special attention into it.

Adam shared good experiences working with sra toolkit and he often time has to try different versions. Therefore, he keeps a list of sar toolkit and kindly shares within the group.

/ddn/gs1/home/burkholderab/bin/fastq-dump.2.0.3
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.1.0
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.1.12
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.1.2
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.1.6
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.1
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.2

Details about fastq-dump options

In the end, different versions of fastq-dump is needed, i.e.

nohup /ddn/gs1/home/burkholderab/bin/fastq-dump.2.1.12   SRR1343625.sra &
nohup /ddn/gs1/home/burkholderab/bin/fastq-dump.2.1.12   SRR1343624.sra &

nohup /ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.1  SRR036616.sra &
nohup /ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.1  SRR036617.sra &
nohup /ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.1  SRR036622.sra &
nohup /ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.1  SRR036623.sra &

nohup /ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.1  SRR1343624.sra &                   
nohup /ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.1  SRR1343625.sra &                   

nohup /ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.1  --split-files  SRR1448790.sra &
nohup /ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.1  --split-files  SRR1448791.sra &

Next, I need to figure out how to dump ERR## files

ERR375885.sra
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.0.3  -X 5 -Z  ERR375885.sra
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.1.0  -X 5 -Z  ERR375885.sra
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.1.12  -X 5 -Z  ERR375885.sra
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.1.2  -X 5 -Z  ERR375885.sra
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.1.6  -X 5 -Z  ERR375885.sra
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.1  -X 5 -Z  ERR375885.sra
/ddn/gs1/home/burkholderab/bin/fastq-dump.2.3.2  -X 5 -Z  ERR375885.sra
fastq-dump.2.4.2  -X 5 -Z  SRR375885.sra

Firstly, let’s understand what does an “ERR” stand for.

Found it at the SRA doc
It turns out easier to download the files directly from EBI
Then, I need to validate the sequence at NCBI

A good tutorial can be found here

A good help link