RNA-SEQ Single End

RNA SEQ Single End App generates a Script file which can be executed on a Cloud or Server. You will have to select the sample information file, organism, output script file and the email. You can additionally  provide Tophat and Cufflinks parameters. Once you click Compile, a script/batch file is generated which can be executed using the Execute App.

RNA-Seq Single End Analysis

Sample Information File

Sample Information File is two columns file separated by tab (Use Excel and save it as txt file. No header is required). The first column is the name you want to give to your sample. The second column is the FASTQ file name. See Example. Please don’t use any space in the names, file name or file path.


Select your organism, If your organism is not listed, select any Organism and once the script file is created, use Replace to change the Organism genome path or alternatively contact us to incorporate your organism.

Tophat Parameters

By default it creates script with minimum parameters. But you can always add more parameters.

Cufflinks Parameters

By default it creates script with minimum parameters. But you can always add more parameters.


Provide your email address. You will receive updates of your analysis on email and also obtain the expression metric (RPKM or FPKM) via email.

For additional information, you can access the server/cloud using FileZilla, WINSCP or FTPBOX

Output Script File

Based on the information Output Script File will be generated. You can make modifications to the Script if you require. Once you are happy with script file, you can use the Execute App to execute the script on the server. A sample Script file using the Sample Information File  can be downloaded.

Additional Information if you are using your own institutional server

This App depends on Bowtie, Tophat, Samtools and mutt. All these software’s should be installed configured and available on path. Additionally, the Bowtie Tophat libraries need to be properly placed on the server. These library files need to be downloaded and placed in a folder by name of igenome in the /usr/local and accessible to all users.


1) I don’t see the window as shown above

Ans: You might not be having latest version of .NET Download and install .NET.

2) I don’t see my Organism.

Ans: Use any Organism, and once your script file is generated change the path to that of your desired organism. If you are using our Cloud, we will provide you the App with the needed organism incorporated.

3) Error

Ans: Likely that your sample information file is in wrong format.



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