Problems with the tutorial data

rna-seq
fastqc
tutorial

#1

Hi. I’m working with the “RNA Seq (RB)” data that appear in the “RNAseq tutorial An introduction”. The problem is that when I try to perform a quality control with FastQC Read Quality Reports I do not get any reading in the section Per base sequence quality. Can someone explain to me why?
Thank you.


#2

If fasta data is input to FastQC, and not fastq, then there would be no quality scores available to evaluate. The most current Galaxy RNA-seq tutorials use fastq data with quality scores.

A bit more information will help to troubleshoot if the above does not resolve the problem:

  1. Is this the tutorial you are following? https://galaxyproject.org/tutorials/rb_rnaseq/
  2. If not, what is the tutorial link?
  3. Where are you running the tutorial? A public Galaxy server? Which (URL)?
  4. Could you share more about the unexpected output from FastQC? A screenshot would help. The first tutorial above does not include a FastQC step, but others do.

#3

Yes, the tutorial is https://galaxyproject.org/tutorials/rb_rnaseq
and the data is in fastqsanger format. I attach a screenshot.


#4

AH, ok, that helps. I had forgotten that the data for this tutorial has dummy (padded) quality scores in the fastq data. It isn’t appropriate data to learn how to use FastQC.

The tutorial is a bit older and also uses Tophat, which has since been deprecated and usually works but sometimes not. The utility of keeping the tutorial active is to review a few basic Galaxy UI functions and how RNA-seq analysis works in general, rather than being a complete workflow with sample data to model after for a complete analysis.

I would suggest either following that tutorial exactly to learn how to use collections and the other basics included. Or, you can skip that tutorial and try the other one listed right below it at https://galaxyproject.org/learn/. It includes QA steps, the right type of example data, the mapping tool HISAT2 (replaces Tophat), and will work at Galaxy Main https://usegalaxy.org.

Then you can explore the RNA-seq and other tutorials from the GTN.

Note: Your Galaxy Help account doesn’t seem to be verified yet. Check your email (including spam/trash) for a verification email/link. This will allow you to post without waiting for moderator approval.


#5

Ok. Thank you very much.