Hi @f_kurt
Please see this prior Q&A, it covers most of what you are asking about. It is worth reviewing first: What to do with trinity output files
For tools that appear to be missing, it could be that the Galaxy server you are working at does not have them installed. Or, the tool panel search is not finding them for some reason (search term typo?). You can also directly check.
Trimmomatic
is often under the tool group “FASTQ Quality Control”. And yes, performing QA is probably a good idea.FastQC
is just a quality report – no changes are made to the data. It is important that both ends of paired-end data are input to assembly, andTrimmomatic
will output pairs that are still paired post-QA.Assemblystats
is available in the ToolShed but is not hosted at all public Galaxy servers.Fasta Statistics
is hosted and is usually under the tool group “FASTA/FASTQ”. Or, you may be more interested inCompute contig Ex90N50 statistic and Ex90 transcript count from a Trinity assembly
in the tool group “RNA Analysis”.
The “Transcriptomics” Topic of the GTN Tutorials covers RNA-seq analysis (but not for all of this exact analysis – is still a work in progress – and explained in the linked Q&A above):
Thanks!