Hello Elsayed, Protocol help for RNA-seq analysis can be found here: https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq The QA/QC steps should be done before mapping, on individual datasets (such as replicates) or on partial or merged datasets as needed (if that is how the data was sequenced, just be consistent). Only keep in mind that the larger the dataset, the more compute some of these steps can require. Hopefully this helps, Jen Galaxy team On 1/1/14 1:32 AM, Elsayed Hejazy wrote:

i need to know more about the order of steps for RNA Seq data analysis Is alignment and assembly should done first to combine all FASTQ reads into one file and start analysis or i should do Quality Control ,filtering , trimming and manipulation first and do alignment and assembly at the end of analysis to use tophat for example or any other analysis tools in Galaxy

Thank you elsayed

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