rna-seq alignment and calculate + compare expression levels

Question

[dimitrischat]

Hello all.

I have fastq files from RNA-seq. i need to do alignment with tophat2 and was wondering what is the command line in terminal , also what is the command line for cufflinks to calculate the expression levels and finally what is the command line to compare the expression levels with cuffdiff. The sequence is from mouse but my question is general so other people can see it too. I use mac / terminal.

Answer 1

[Benn]

Did you check the published protocols? For instance in Nature protocols there are many examples of codes.

http://www.nature.com/nprot/journal/v7/n3/full/nprot.2012.016.html

Answer 2

[Carlos Caicedo]

Hi

Have you ever thought about use Galaxy ? All the tools that you mentioned are available there and you do not need to use command line.

Regards

[dimitrischat]

no idea what that is .. could you tell me some info

[Carlos Caicedo]

Hi

From Wikipedia: Galaxy is a scientific workflow, data integration, and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience. Although it was initially developed for genomics research, it is largely domain agnostic and is now used as a general bioinformatics workflow management system.

The web page is: https://usegalaxy.org/ You have to create an account.

The platform is described at: https://genomebiology.biomedcentral.com/articles/10.1186/gb-2010-11-8-r86

This is a forum where you can put your questions: https://biostar.usegalaxy.org/

Regards.