Help us improve our Training Material

Help us develop the best training material for RNAseq analysis !

Dear community, the Galaxy team is working on a set of tutorials dedicated to RNAseq analysis. To serve community better we would like to prioritise our tutorial development. We want to do this by asking you what flavors of RNA-seq are in highest demand. To do this we prepared a short overview of various RNA-seq types:

Rna seq graph
Figure 1. : RNA seq analyses process

From you reads data (in purple), two paths can be followed depending on the available references (in green). If an existing transcriptome is available, you can map the read on the transcriptome and perform a quatitative analysis based on the read counts. If no transcriptome is available you need to assemble one. If a Genome is available, you can assemble the transcriptome by mapping the reads on the genome, otherwise you have to performe a denovo transcriptome assembly. Once you have assembled your transcriptome, you can perform your quantitative analysis using the read counts.

Another way to look at this is the following table :

Reference availability Tools
Genome Transcriptome Assembly Mapping/count
Hisat/StringTie Kallisto/Salmon
Hisat/StringTie Hisat/StringTie
TRinity/RNASpades Kallisto/Salmon
Kallisto/Salmon
Table 1 : Tools for mapping and assembly, depending on reference availability

So, here is what we want from you:

  1. Are we missing anything?
  2. What tutorials do you want to see developed first? Use this Poll to answer!

Thank you for your help!