Rna-Seq Paired End Analysis

Question

[KS]

Hello everyone,

I am trying to do RNAseq analysis on Paired end data Illumina. I have about 4 files for each sample (2 forward and 2 reverse).

I want to analyze the data in Galaxy.

Do I have to groom and run the QC for each file? Should I join the paired files and run both tools on each pair, or should I combine all of the data for each sample (which I don't know how to do) and then groom and run the QC for all of the reads for the sample.

Ultimately, How do I run TopHat for paired-end data. When I select paired end data in Galaxy, it gives an option to upload both files should I upload both forward files once and reverse files once. Or should I combine both the files before running the TopHat.

I am all confused. Any kind of help will be appreciated

Thanks in advance

Answer 1

[seidel]

Have you explored the Galaxy site for documentation or examined any published workflows? Take a look at some of the workflows. There is a lot of information there. You might also try experimenting with your data. Sometimes if you can't figure it out from the documentation it's the best way to proceed, or will at least help narrow the line of questions. From your description it sounds like you haven't tried anything yet.