From SRA to differential genes in Galaxy

[Fay]

Dear all,

I want to analyze SRA files from a paper, and see how is the RNA library quality (uniquely map gene percentage, etc). Could you provide step by step guidance how to do it?

I have downloaded SRA files from the paper onto galaxy, as “pasted entry”. Then I use the “faster download and extract reads in fastq, format from NCBI sra” tool to extract reads. After this task is done, “Paired-end data (fastq-dump)” is shown in the history as finished.

With these files, I want to do FastQC, and align the files with STAR, then do post-alignment QC to check the unique align percentage. What are the steps to do these task? I would greatly appreciate if someone can help with this, the more specific about the steps the better.

Many thanks in advance!

Cheers,
Fay

[jennaj]

Welcome, @Fay

Please see this tutorial:

Galaxy Training: RNA-Seq reads to counts

Additional tutorials for RNA-seq analysis are one level up in the topic Transcriptomics. If you are completely new to Galaxy, going through a few of the Introduction tutorials first may be helpful.

Workflows are available for all tutorials – and each can be imported and further customized, or simply reviewed as examples as you learn to create (or extract) your own for ongoing analysis purposes.

@jennaj

Galaxy Training Network Tutorials : Some GTN tutorials are appropriate for Galaxy Main and some are not. Where you can run each is noted per tutorial – click on the Galaxy instances gear icon to review the Public Galaxy server choices. If a tutorial is supported by a pre-configured Galaxy Docker training image, instructions for how to get it will be listed below the tutorial listings, per category.

Thanks!