Greetings all,

I'm trying to build out a Galaxy workflow to support trinity rna-seq
de novo assembly and all the various downstream analyses.  For the
initial trinity de novo assembly, I took Jeremy's initial workflow and
tweaked it to work with the latest release - and submitted it to the
galaxy tool shed.  So, step 1 is done.  But... here's what I'm
ultimately trying to accomplish:

Given fastq files for a number of different samples {A,B,C}

1. merge {A,B,C,...} =>  MERGED.fq
2. run Trinity based on MERGED.fq to generate Trinity.fasta (existing
workflow does this already)
3. align the original {A,B,C,...} separately to Trinity.fasta using bowtie
4. for each alignment, perform abundance estimation
5. combine results from each abundance estimation into a matrix file
6. run some Bioconductor tools to analyze differential expression

There are some complexities here, such as not knowing ahead of time
how many different samples are to be processed - so this needs to be
determined dynamically, which impacts the overall complexity of the
total workflow.  Is this possible in Galaxy, and if so, are there
examples I can work from?

There are a whole bunch of other add-ons I'd like to include beyond
the above, but I figure that if the above is doable, then the rest
should be equally doable.

Many thanks!
Brian J. Haas
Manager, Genome Annotation and Analysis, Research and Development
The Broad Institute
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