DeNTAS :De Novo Transcriptome Analysis & Statistics

This file contains a basic description of DeNTAS' analysis pipeline, details of the softwares requirements and user instructions to run the program from a local machine. Please see the DeNTAS's documentation for further information <link here?>

DeNTAS Summary

DeNTAS is a software tool for the statistical analysis and visualisation of Transcriptome datasets generated by de novo assemblies of RNA-seq datasets.

User input:

1. Raw assembled transcripts in FASTA format with FPKM values
2. Organism that samples were derived from
3. Experimental groups from the samples

Analysis:

1. Identification of transcripts via local blast on Apocrita (QMUL's high performace computing cluster)
2. Differential gene expression analysis and statistics conducted in R using the limma package

Results returned:

1. Unsupervised data exploration: Principla component and hierachical clustering (dendrograms) plots both for the full set of genes and for the subset of genes determined to be significantly differntially expressed
2. Volcano plots depicting each experimental comparrison. Those genes that have a logFoldChange > 2 and an adjusted p-value < 0.05 are highleted in red and labelled
3. Heatmap depicting the top 100 differntially regulated genes
4. Interactive table listing all differential regulated genes, by refseq ID, gene symbol, full gene name and showing their e-value for each experimental comparison

Setting up the local server

DeNTAS harnesses the power of high performance cluster computing to increase the speed of analysis. Therefore execution of the software on a local machine has the following requirements the user must:

1) Have secure access to Apocrita without the need for a pasword

>> ssh-keygen (hit enter 3 times)

>> ssh-copy-id <username>@login.hpc.qmul.ac.uk (input your apocrita password)

>> ssh <username>@login.hpc.qmul.ac.uk (test connectivity)

2) Utilise this secure access to enable direct connection to the remote-server, Apocrita, when the app is run.

This needs a one-time setup on the user device. Once the user has obtained the app folder, they must make the specific change of the code text "" to reflect their own apocrita username to all of the script files found in the "> app/scripts/apocrita" directory.

This can be performed with ease through an appropriate text editor which is capable of detecting multiple instances of the word "" and enables the user to multi-word edit each instance (for example, 'Sublime' offers this functionality).

Running DeNTAS

Now that the local user machine has been set up as a local server with direct connection to the remote server (apocrita), the user can execute the app through the terminal by going into the app's directory and using the following command:

python app.py

How to Use DeNTAS Well

The user should submit appropriate de novo transcriptome data with the known FPKM values in order for DeNTAS to function effectively.

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