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rna-seq alignment and calculate + compare expression levels

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.

rna-seq
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updated by Carlos Caicedo Carlos Caicedo • written by dimitrischat dimitrischat

2 answers

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

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written by Benn Benn

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

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written by Carlos Caicedo Carlos Caicedo

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

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written by dimitrischat dimitrischat

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.

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written by Carlos Caicedo Carlos Caicedo

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