ShortRead output

[rakscalloni]

Hello everyone!

I am a very beginner in RNASeq data analysis and used ShortRead to assess the reads quality. However, I need some help to understand/interpret the ShortRead output. Therefore, I would like to ask you for basic literature about parameters commonly used to certify the sequencing quality. I guess this kind of reading could help me with the ShortRead output...

Thanks

[blancha]

Why not use FASTQC? The output is easy to interpret.

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Or do you have a reason to use ShortRead over FASTQC?

[rakscalloni]

Why not use FASTQC? The output is easy to interpret.

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Or do you have a reason to use ShortRead over FASTQC?

Hi Blancha!

Actually, I am following the pipeline proposed by this article "Count-based differential expression analysis of RNA sequencing data using R and Bioconductor", and the authors suggested ShortRead to check the reads quality. As I started with RNA-Seq analysis two weeks ago, I am not fully informed about the programs options.

I intend to learn how to use both ShortRead and FASTQC...

Thank you for your help