mRNA-seq data analysis

[smsm]

Hi everyone, It is my first time to use mRNA-seq protocol. I got my sequencing data back but I am really stuck in the analysis. I want to compare the gene expression level in the mutant with that in the wildtype. I used scanseq to analyze the data. However, I do not know if the results are real or not.
I would really appreciate it, if anyone can help me with these analyses.
Thanks!

[shurjo]

I am not familiar with scanseq, but have been using ERANGE and Cufflinks for gene expresssion analysis. What is your level of comfort with command-line tools and UNIX in general?

[smsm]

Thank you for your replay! I am not really familiar with UNIX and I do not think anyone in my lab is familiar with ERANGE or Cufflinks. Is it easy to use them?

[shurjo]

It might be a bit complicated to get the maximum possible benefit from ERANGE and Cufflinks if you are totally unfamiliar with UNIX-based systems. However, you could try commercial packages such as Partek Genomics Suite or Genesifter. These were designed for allowing entirely experimental labs to comfortably analyze NGS data. I have had some experience with both these software packages and would say that they are both very user-friendly, at the cost of losing some of the flexibility you would have if you had a bioinformatician in your group who could write custom scripts based on your needs.

[RockChalkJayhawk]

Thank you for your replay! I am not really familiar with UNIX and I do not think anyone in my lab is familiar with ERANGE or Cufflinks. Is it easy to use them?

You might want to learn UNIX and a little perl. A good place to get started is this PDF I have attached and join the Google group http://groups.google.com/group/unix-...for-biologists. Spend a couple of weeks getting the basics and it will do you a world of good.

I taught myself using this and other available resources on the web. Also, you can download Linux distributions for FREE and have it and your current operating system on the same computer. All of the latest-and greatest analysis softwares are open source and many are only compatible with Linux.

By the way, it also makes you a more valuable resource. I am the only person in my department that can run Linux and do any of the analysis. Like I said...it will be worth it.

[RNA-seq]

I recommend Partek. It is very user friendly. You don't have to learn programming and you can analyze your data with button clicks. For RNA-seq data, it can do differential expression and alternative splicing analysis. It also has the function to detect novel transcripts and identify SNPs. It is worth trying.

[alaincoletta]

You can upload your fastq files to https://insilicodb.org. The tophat - cufflinks - cummerbund pipeline will be executed. The data will be analysis ready.